The Spirit of Christ had no gender
Paul used the generic “WHO” to describe Christ in 1 Timothy 3:16, and Philippians 2:6, because the Spirit of Christ, in the Old Testament had no gender.
In fact, the Spirit of Christ was only described using feminine verbs and pronouns in the Old Testament.
Jesus was not “the Son” in the Old Testament. Jesus never used the expression “My Father” when referring to God who sent Him, as we read throughout John.
Christ was first called “the Son” at His Baptism
The first time that Jesus was called the Son of God, was during His baptism. The Spirit of God descended on Him, and a voice was heard from heaven, saying “You are My beloved Son; in You I am well pleased.”
Paul told us that Christ was “justified in Spirit.” Justification simply means the right to be called a Child of God. Normally we say that a new believer is “sanctified by the Spirit,” but Christ was already the sanctified Holy Spirit of the Old Testament.
The Phrase: “Only Begotten Son” was a Forward-Looking Expression
The expression “only begotten Son” compared Abraham to God. Abraham was willing to sacrifice his only son, whom he loved. God spared the life of Abraham’s son, but not His Own. This was God’s plan of salvation, and therefore, John said that Jesus was “the Lamb slain from the foundation of the world” (Revelation 13:8).
Jesus Himself also described this plan as if it had already been fulfilled, when He said:
“For God so loved the world that He gave His only begotten Son, that whosoever believeth in Him should not perish but have everlasting life.” (John 3:16)
Christ became “the Only Begotten Son” when He resurrected
We may all become the Sons of God when the Spirit of Adoption descends on us, but Jesus Christ is still God’s only begotten Son.
Paul told us that Jesus became God’s only begotten Son when God resurrected Him as a new spiritual being:
“God has fulfilled this for us in their children, in that He has raised up Jesus. As it is also written in the second Psalm: You are My Son, Today I have begotten You.” (Acts 13:33, and Romans 1:4)
Psalm 89:27 also prophesied that Christ would be resurrected as the firstborn and as our Lord: “I will make Him My firstborn, the highest of the Kings of the earth.”
Therefore, the Apostle John in Revelation 1:5, called Jesus Christ: “The firstborn from the dead, and the ruler over the kings of the earth.”
In Revelation 21:7, God promised that we will also become the true Sons of God, if we also overcome.
“I will be his God and he shall be My son.”