John 1:1 predates Gen 1:1. Before there was a universe God existed. He created a Spiritual creation evidenced by this...
Rev 11:19 Then the temple of God was opened in heaven, and the ark of His covenant was seen in His temple. And there were lightnings, noises, thunderings, an earthquake, and great hail.
Now we read this...
Heb 8:4 For if He were on earth, He would not be a priest, since there are priests who offer the gifts according to the law;
Heb 8:5 who serve the copy and shadow of the heavenly things, as Moses was divinely instructed when he was about to make the tabernacle. For He said, "SEE THAT YOU MAKE ALL THINGS ACCORDING TO THE PATTERN SHOWN YOU ON THE MOUNTAIN."
So everything that Moses made (or had made) concerning the Tabernacle predated this time in heaven. The physical creation could well be 14.5 billion years old as we are told, the Biblical account allows for that. but the Spiritual creation predates all.
Now John 1...
Joh 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.
Joh 1:2 He was in the beginning with God.
Joh 1:3 All things were made through Him, and without Him nothing was made that was made.
So Christ was with the Father prior to verse 3 when ALL things were made, both Spiritual and physical.