1 Corinthians 6:16 - What? know ye not that he which is joined to an harlot is one body? for two, saith he, shall be one flesh.
1 Corinthians 12:12 - For as the body is one, and hath many members, and all the members of that one body, being many, are one body: so also is Christ.
Ephesians 2:16 - And that he might reconcile both unto God in one body by the cross, having slain the enmity thereby:
Ephesians 4:4 - There is one body, and one Spirit, even as ye are called in one hope of your calling;
Colossians 3:15 - And let the peace of God rule in your hearts, to the which also ye are called in one body; and be ye thankful.
Ephesians 5:31-32 - For this cause shall a man leave his father and mother, and shall be joined unto his wife, and they two shall be one flesh. This is a great mystery: but I speak concerning Christ and the church.
Phiz- If you meditate on these scriptures above. You will see that we become one spirit with Him. As you pointed out, Christ prayed that we'd have the same oneness with Him and the Father that He has. Paul says just as the husband and wife are made one flesh, so shall Christ and the Church.
When the man enters the woman, they become one. They are no longer separated. Likewise, when the Lord enters us, we become one with Him and therefore, no longer separate...
1 John 1:7 - But if we walk in the light, as he is in the light, we have fellowship one with another, and the blood of Jesus Christ his Son cleanseth us from all sin.
May God give grace...
With Love,