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The word in could prove to be quite a puzzle because, if we understood it as "inside" rather than "in union with," we would have God and Christ crawling inside and out of each other. It would create a farcical, "Where is He now? The Son is in the Father. No, the Father is in the Son." Or, because Christians are included in verse 20, it would be, "No, He's in me." "No, He's in you." Or, "No, I'm in Him." We could get all confused. But God is logical.
Here, the sense is definitely "in union with." The Father and Son are two separate Beings who sit side by side in carrying out the responsibilities of providing for and maintaining the operation of His creation both physically and spiritually. When the Son was on earth, He was in union with the Father, and the Father was in union with Him.
It is almost as if they were—well, humanly, we would say "one flesh." When a man and a woman marry, are they two different beings? Yes, they are. Are they commanded by God to marry for the purpose of becoming one, in union with each other? Yes (Genesis 2:24).
Do they crawl in and out of each other? No, of course not. Nevertheless, a blending takes place: a blending of mind and personality. And what eventually happens? It is something that begins even before the two become married. No matter where one of them goes, because of their experiences together, he or she carries the presence of the other with him or her, and they can call up those memories in the blink of an eye. Is that not simple?
The same principle is involved in the union of the Father and the Son—and the union of God and the Christian.
John W. Ritenbaugh
Image and Likeness of God (Part 4)