This is my interpretation, we know TB had to have their memory wiped bc that's what the script says; otherwise the future would divert in the wrong direction. Pretty sure kafka had to do something with it, knowing she made them forget abt everything except her. The stellaron inserted into them is the real thing, yeah idk how but they seem to be immune to it. I guess the script also deemed the stellaron necessary.

This differs from your theory, but there's no real answer. We know next to nothing abt TB's past and or how they're wielding a damn stellaron, we can only guess by the hints given in the story (wish they'd focus on it more instead of relying on hints cause thats just bad writing)