That is not clear. Did YHWH become the Son or did YHWH live in the Son (a totally separate being) through His indwelling Holy Spirit?
Yahweh Elohim was a spirit entity. He was the firstborn spirit Son of Elohim (Colossians 1:15 and Revelation 3:14).
Yahweh Elohim from the beginning loved righteousness and hated iniquity (Psalms 45:7).
Therefore Elohim elevated Yahewh Elohim to Godhead and anointed his head with the oil of gladness above his fellows (fellow or brother spirits). Only Yahweh, the firstborn fellow remained sinless from the beginning.
Elohim also invited Yahweh to sit on his right hand
(Psalms 110:1) and gave him power and authority to make the physical heavens and earth and all that are in them (John 1:1-3)
Yahweh was also the Word of God.
He was with God from the beginning, being His firstborn spirit Son.
He was eventually given power and authority to make all things.
Yahweh Elohim through all this history was in a spirit form. When it came time for Yahweh to save mankind, he was sent by Elohim to the earth and his own personal spirit took on flesh and bone, and he became a mortal man.
So the incarnation is not the HS coming to dwell with Jesus. There truly was an incarnation, his own personal spirit (now a deity) was housed in a body of flesh and bone, and he became a living mortal soul.
Elohim was still with him as He sent the HS to abide with Yahweh (now Jesus) also, and he was able to accomplish his mission and atoned for the sins of all mankind (being deity and able to do that). Was resurrected with a body of flesh, bone, and spirit, and now sits again at the right hand of Elohim, and has been rewarded with the same glory that he had before the world was created (John 17:5).
It all fits logically. It all fits biblically. It is the truth.
The Scriptures teach that God cannot die. He has inherent immortality which He gave to His Son. Therefore, He could not make the Atonement. The Atonement was a sacrifice MADE TO GOD, not made BY God.
Elohim cannot die, but the scriptures say that His Son Yahweh/Jesus did die and was sacrificed to God (the last great sacrifice) so that mankind could be reconciled to Elohim, if they believe on the Son.
John 17:5 does NOT say Yeshua was a "deity". You are reading that into the text as usual. The glory Yeshua had before the world was is as the "Lamb slain" before the foundation of the world.
So you think the glory that Jesus was asking for was the glory of the 'Lamb slain' before the foundation of the world? Well, I guess that is a glory Jesus had. But I think you are reading as much into scripture as you say I am, trying hard to get around John 17:5. Good try, but I like the glory that I believe in, that Jesus was the creator of all the physical heavens and earth and sat next to Elohim, and was also the 'Lamb slain' before the foundations of the world. He was a God before his earthly ministry, during his earthly ministry and asked and received that same glory after his earthly ministry.
If he was a deity, was he miniaturized into an embryo?
Good question. One that we cannot answer, not knowing the science of the spirit entering the body and all.
But we do know that the HS miniaturized himself and abode in the body of John the Baptist from his mothers womb (Luke 1:13-15). So the miniaturization process is not an unknown to Elohim and so Yahweh's spirit entered into the body of Jesus while he was in his mothers womb, just like the HS entered into the body of John the Baptist while he was still in his mothers womb.
Very interesting science.