The Vision of the Brother of Jared
It is important to note that in Ether chapter 3 in the Book of Mormon, the "body of spirit" that is mentioned therein is not the Father who is a "personage of spirit" (described in Lecture 5). In other words, Ether 3 is not the Father-Jehovah appearing. Instead, Ether 3 is a vision where the Brother of Jared is being visited by the actual earthborn Jesus but before he was born. In Mormon scriptures, certain stones provide the seer the ability to see the future. So after the "Lord stretched forth his hand and touched the stones one by one with his finger" it was then that "the veil was taken from off the eyes of the brother of Jared" so he see in a vision the not yet born earthly Jesus in a dreamlike vision. For the veil was lifted from his natural eyes so he could see into the future like a seer (see Ether 3: 6, 19); so that in a dream-like vision he sees and talks to the the future earthborn resurrected Jesus with nail marks in his hands looking just as he would later appear as the resurrected Christ appearing to the Nephites in 3 Nephi.
Here is Ether 3: 6-18 (emphasis added):
6 ... when the brother of Jared had said these words, behold, the Lord stretched forth his hand and touched the stones one by one with his finger. And the veil was taken from off the eyes of the brother of Jared, and he saw the finger of the Lord; and it was as the finger of a man, like unto flesh and blood; and the brother of Jared fell down before the Lord, for he was struck with fear.
The brother of Jared then says in verse 8, "I knew not that the Lord had flesh and blood." Obviously he is not seeing the actual earthborn Jesus as this would have been before Jesus was born to become a body of flesh and blood. So he is only seeing a kind of hologram of a body that is like unto [the] flesh and blood body of the earthborn Jesus. The chapter then continues:
9 And the Lord said unto him: Because of thy faith thou hast seen that I shall take upon me flesh and blood [note the future tense]; and never has man come before me with such exceeding faith as thou hast; for were it not so ye could not have seen my finger. ... 13 And ... behold, the Lord showed himself unto him, and said: Because thou knowest these things ye are redeemed from the fall; therefore ye are brought back into my presence; therefore I show myself unto you.
14 Behold, I am he who was prepared from the foundation of the world to redeem my people. Behold, I am Jesus Christ. I am the Father and the Son [compare Mosiah 5:1-5]. In me shall all mankind have life, and that eternally, even they who shall believe on my name; and they shall become my sons and my daughters.
15 ... Seest thou that ye are created after mine own image? Yea, even all men were created in the beginning after mine own image.
16 Behold, this body, which ye now behold, is the body of my spirit; and man have I created after the body of my spirit; and even as I appear unto thee to be in the spirit will I appear unto my people in the flesh.
Note how verse 15 matches what Smith would later compose as additional scripture in Moses 1: 1 - 6, wherein Moses too has a visionary experience: as "Moses was caught up into an exceedingly high mountain, and he saw God face to face, and he talked with him ..." (verse 1-3). Then Moses also sees in a visionary state the future, as Father-Jehovah says to Moses in Moses 1: 4-5, "And, behold, thou art my son; wherefore look, and I will show thee the workmanship of mine hands; but not all, for my works are without end, ... Wherefore, no man can behold all my works, except he behold all my glory; and no man can behold all my glory, and afterwards remain in the flesh on the earth." Then we come to verse 6:
6 And I have a work for thee, Moses, my son; and thou art in the similitude of mine Only Begotten; and mine Only Begotten is and shall be the Savior, for he is full of grace and truth; but there is no God beside me, and all things are present with me, for I know them all.
As covered above, the word "Son" here only refers to the fleshly bodily image of and future status of the the earthborn Jesus as the Savior. We see the same idea being repeated in Ether 3: 15:
... Seest thou [brother of Jared] that ye are created after mine own image? Yea, even all men were created in the beginning after mine own image.
And so what Image is all men created after? The answer is given in Moses 1: 6:
... Moses, my son; and thou art in the similitude [likeness] of mine Only Begotten; and mine Only Begotten is and shall be the Savior, for he is full of grace and truth; but there is no God beside me ....
So if we combine Ether 3: 15 and Moses 1: 6 (quoted above), we can see that Father-Jehovah forms all humans in the image of the earthborn Jesus who would become the Savior.
Ether 3: 16 then explains in 1830 what would be later on better explained in 1835 with the doctrine of Lecture 5. So let's now look at Ether 3: 16 (emphasis added):
Behold, this body, which ye now behold, is the body of my spirit; and man have I created after the body of my spirit; and even as I appear unto thee to be in the spirit [in a vision] will I [actually] appear unto my people in the flesh.
We know this body is not the actual earthborn Jesus. We know its not the Father. We know this is a kind of hologram of the earthborn Jesus. So what is this body of spirit God uses to create man? The answer is in Moses 1: 6:
... Moses, my son; and thou art in the similitude [likeness] of mine Only Begotten; and mine Only Begotten is and shall be the Savior ...
We see here based on LDS Scripture itself that the body of spirit is Father-Jehovah's Only Begotten, which is the bodily image or prototype of the future earthborn Jesus, the Savior.
Lecture 5 further explains all of this in the Q&A section (emphasis added):
Question 7: What is the Son?
First, he is a personage of tabernacle [flesh]. (5:2)
Question 8: How do you prove it?
John 14:9-11: Jesus says unto him, Have I been so long time with you, and yet have you not known me, Philip? He that has seen me has seen the Father; and how do you say then, Show us the Father? Do you not believe, that I am in the Father, and the Father in me? The words that I speak unto you, I speak not of myself: but the Father that dwells in me, he does the works. Believe me that I am in the Father, and the Father in me. Secondly, and being a personage of tabernacle, [Jesus] was made or fashioned like unto man, or being in the form and likeness of man. (5:2) Philippians 2:5: Let this mind be in you, which was also in Christ Jesus; who being in the form of God, thought it not robbery to be equal with God; but made himself of no reputation, and took upon him the form of a servant, and was made in the likeness of man, and, being found in fashion as a man, he humbled himself, and became obedient unto death, even the death of the cross. Hebrews 2:14, 16: Forasmuch then as the children are partakers of flesh and blood, he also himself likewise took part of the same. For verily he took not on him the nature of angels: but he took on him the seed of Abraham. Thirdly, he is also in the likeness of the personage of the Father. (5:2) Hebrews 1:1-3: God, who at sundry times, and in divers manners, spake in time past to the fathers, by the prophets, has in these last days spoken unto us by his Son [tabernacled/enfleshed body], whom he has appointed heir of all things, by whom also he made the worlds; who, being the brightness of his glory, and the express image of his person [i.e. the spirit personage of Father-Jehovah]. Again, Philippians 2:5-6: Let this mind be in you, which was also in Christ Jesus; who being in the form of God, thought it not robbery to be equal with God.
16 Behold, this [holographic] body, which ye now behold, is the body of my spirit [as a prototype image seen as the express image of the spirit personage of Father-Jehovah per Lecture 5]; and man have I created after the body of my spirit [i.e. this bodily prototype]; and even as I appear unto thee to be in the spirit [i.e. even as I appear to be real in the realm of the spirit in your vision] will I [actually] appear unto my people [for real] in the flesh.
17 And now ... I, Moroni ... it sufficeth me to say that Jesus [as a kind of hologram seen in a vision] showed himself unto this man in the spirit [in a vision beyond the veil in the realm of spirit, the hologram of Jesus appeared as the express image of the spirit personage of Father-Jehovah, as the holographic body of the earthborn Jesus], even after the manner and in the likeness of the same body even as he showed himself unto the Nephites [in Nephi chapter 3 as the resurrected Lord].
What Ether 3 is conveying is that the Godhead always manifests in bodily form as a the image or prototype of Jesus. As a Lecture 7: 9, 16 makes clear below that Christ is the bodily prototype of the one Deity (emphasis added):
9 ... all will agree in this that he [Christ] is the prototype [... of a] saved being. And if we should continue our interrogation, and ask how it is that he is saved, the answer would be, because he is a just and holy being; and if he were any thing different from what he is he would not be saved; for his salvation depends on his being precisely what he is and nothing else; for if it were possible for him to change in the least degree, so sure he would fail of salvation and lose all his dominion, power, authority and glory, which constitutes salvation; for salvation consists in the glory, authority, majesty, power and dominion which Jehovah possesses, and in nothing else; and no being can possess it but himself or one like him: Thus says John, in his first epistle, 3:2 and 3: Behold, now we are the sons of God, and it doth not appear what we shall be; but we know, that when he shall appear we shall be like him; for we shall see him as he is. And any man that has this hope in him purifies himself, even as he is pure.—Why purify himself as he is pure? because, if they do not they cannot be like him.
... 16 These teachings of the Savior must clearly show unto us the nature of salvation; and what he proposed unto the human family when he proposed to save them—That he proposed to make them like unto himself; and he [Jesus] was like the Father[-Jehovah, a personage of spirit/nooma], the great prototype of all saved beings: And for any portion of the human family to be assimilated into their likeness [Father and Son] is to be saved; and to be unlike them is to be destroyed: and on this hinge turns the door of salvation.
First note that in Lecture 7, salvation is equated with the current Mormon concept of exaltation, as in having all power and glory that Jehovah possesses. Note as well that in the verses above, Father-Jehovah, as a "personage of nooma," is the great prototype of all saved/glorified beings. In other words, the omniscient Deity of Lecture 2, foresaw the tabernacled/earthly form of Jesus (the Only Monogene), and then formed for himself a personage composed of a spiritual/heavenly substance (i.e. nooma), and that became the template or prototype of all saved or exalted beings; and then Christ was born in human form as the "prototype made flesh," so that Jesus as the twin genome of Father-Jehovah, became the prototype of just and holy beings; holy meaning made divine in order to inherit the same power, glory and dominion as Jehovah.
When Old Testament prophets saw God in bodily form they saw the noomatic body of Jehovah as a genomic twin copy of Jesus (before Jesus was born). The Brother of Jared was simply given a special kind of vision where he saw in a dream-like vision the actual earthborn Jesus with a crucified body as the resurrected Christ but before Jesus had even been born. Here is my visual again putting all of this together:
So the Father as a personage of spirit in Lecture 5, is not to be confused with the mere holographic appearance of the earthborn resurrected Jesus in Ether 3, which is only a kind of holographic form of the not yet earthborn body of Jesus.
So to recap: there is Jehovah's actual "personage of spirit" explained in the the 5th Lecture on Faith, which is in the form of a Man as a personage of spirit, a body composed of pneuma (again, pronounced nooma), meaning it's a body composed of spiritual matter or a heavenly substance. This is not the "body of spirit" described in Ether 3. In Ether 3, the brother of Jared is only experiencing an "appearance" of the risen Lord (the earthborn Jesus as a resurrected body) with nail marks in his hands, so he is only seeing Jesus as he will later appear in the flesh on earth, so it is clearly a vision where he is seeing the earthborn fleshly Jesus but before Jesus was even born in the flesh; and thus it is not the actual earthborn Jesus (but a vision of the future Jesus).
Again, what appears to the brother of Jared in Ether 3, is not the actual resurrected Jesus (as Jesus had not been resurrected yet), but it is a vision of the resurrected Jesus before Jesus is even born; and thus it is meant to be interpreted as someone in Old Testament times seeing the resurrected Jesus in a dream-like visionary state; as the brother of Jared even talks with the risen Jesus yet it is obviously not the actual resurrected Jesus as that Jesus (the "resurrected Lord") does not become a reality until later in the text when Jesus with a resurrected body actually appears to the Nephites in 3 Nephi. This is why in Ether 3: 17, Moroni says the following (my words in brackets):
"... Jesus showed himself unto this man [the Brother of Jared] in the spirit [i.e. in a dream-like visionary spiritual state of mind], even after the manner and in the likeness of the same body [the same resurrected body, nail marks and all] even as he showed himself unto the Nephites [referring to when Jesus would later visits the Nephites, centuries later in 3 Nephi in a resurrected body after being crucified in the flesh and rising from the dead]."
Thus, we can see that, again, the tangible noomatic body of Father-Jehovah (composed of nooma as described in the Fifth Lecture) is is not who appeared to the brother of Jared in Ether 3.
