So, to you, when you read that Jesus Christ is the Only Begotton of the Father--your response seems to be "but not really."Yes that they were always in Father Son relationship. Even you believe this prior to Christ's incarnation.
Actually I answered it here
God can create by simply speaking it into existence. We aren't given any details such my answer is simply my opinion but God could have created an embryo without using any of Mary's chromosomes.
So, then why did Mary need to be overcome by the Holy Ghost--why not just produce a body the way Adam was produced or just the regular way a baby was produced and then implant in that body the spirit of God? And then why say "the only begotten" if it really wasn't the "begotten" Son of God?