I was thinking along the same lines, though I was thinking about one of the last 'rumoured' trailers (and whatcha know the full one comes out).
At the end it mentioned Sora going into a room full of Unknowns whom all turn towards him at the same time and the Superior emerges from a stairwell above. And thats where Sora is in shock when the leader unhoods himself yada yada...
Now I was thinking, wait a minute, a room FULL of unknowns?
I took it that across the game that Sora would eventually take out each member one by one, even if it;s not on the original world they met, because it's been confirmed that some will move location.
Now then, either Sora doesn't beat any of the dudes up until this point or they are like you theorise, being replaced like the fallen CoM members...
Either that, or that scene has been falsely protrayed.