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fredman said:
To attempt to answer Pilgrim's question specifically, John's treatment on this is found in his commentary on Hebrews where he addresses 1:5. Let me summarize from selected quotations from his commentary:

"Though his sonship was anticipated in the OT (Prov. 30:4), He did not receive the title of Son until He was begotten into time. Prior to time and His incarnation He was eternal God with God. The term Son has only to do with Jesus Christ in His incarnation. It is only an analogy to say that God is Father and Jesus is Son - God's way of helping us understand the essential relationship between the first and second Persons of the Trinity....He is no "eternal son" always subservient to God, always less than God, always under God. Sonship is an analogy to help us understand Christ's essential relationship and willing submission to the Father for the sake of our redemption." Hebrews pp. 27, 28

J. C. Philpot, in his book "The True, Proper, and Eternal Sonship of the Lord Jesus Christ, The Only Begotten Son of God", refutes this argument of the incarnational sonship advocates:

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You say, "I cannot receive the doctrine that Jesus is the eternal Son of God because it denies His co-eternity and co-equality with Him, for a father is necessarily prior to a son, and a father is necessarily superior to a son." Certainly, if we carry earthly reasonings into the courts of heaven, and measure the being and nature of God by the being and nature of man. But the very idea of eternity excludes priority and posteriority of time, and the very nature of God excludes superiority and inferiority. When, then, we say that Jesus is the eternal Son of God we declare His co-eternity, and when we say that He is the Son of God, as God the Son, we declare His co-equality with the Father and the Holy Ghost. But you and the Socinian really stand on the same ground—the ground of natural reason and carnal argument. He draws a natural conclusion that three cannot be one, and therefore rejects the Trinity; you draw a natural conclusion that a father must Exist before, and be superior to, his son, and as you believe the Lord Jesus to be a Person in the Godhead, you therefore reject on that ground the eternity of His Sonship. Thus, neither he nor you submit your mind to the Scriptures. You both really stand upon infidel ground, for both of you prefer your own reasonings and your preconceived notions to the truth as revealed in the Word of God. That speaks again and again of "the only-begotten Son of God," which, as we shall by-and-by show, refers to His divine nature, as in the following passage: "And the Word was made flesh, and dwelt among us; and we beheld His glory, the glory as of the only-begotten of the Father, full of grace and truth" (John i. 14).