While I can see a certain level of applicability to the first two points you mention, I think the most meaningful and relevant answer is something else entirely.
If you look at the at-one-ment of Jesus Christ, in terms of what Jesus taught in the intercessory prayer (John 17:20-23), you can see that he is calling for union to take place between those who are believers.
When you look at the structure of what Jesus Christ organized, you can see a system of ordinances that have covenants coupled with them. Just as a man and a woman enter into a marriage covenant and become "one flesh" so too do believers who join together in a body form a body of one flesh.
So, as I see it, the concept of "one flesh" means that multiple individuals join together in covenant and are organized into some kind of a greater collective identity that can be looked at as its own distinct individual entity.
The marriage between a man and a woman is simply one example of it on one level, but the underlying concept is applicable on a more universal scope at varying levels.
Paul teaches another example of this where in Ephesians 5:30 he says that everyone who joined the Church of Christ is a member of the body of Christ, of His flesh and of His bones.
And, in actuality, as members of the church they are members of the body of the Bride of Christ. But, since Christ and His Bride are married and "one flesh" then Christ can say of the church members that they are "bone of my bone and flesh of my flesh" just as Adam said to Eve. (Genesis 2:23)