the biggest question in this fucking movie after watching it is that where the fuck does Jane/John/Baby come from???? because the baby is her (chicken/egg type of question) but you know its basically a plothole. i can probably make sense of the rest of the movie by making assumptions but there's got to be a starting point unless she really was an orphan and the roberts guy (swaps baby) just tricked him/her unto believing she/he is the baby to prevent her/him from finding the real baby(isn't hard to do when you can fucking time travel and also to avoid a connection that would prevent him/her from being attached)

to answer your original question, i thought of the idea that she originally gets impregnated by a different man, lost the baby, becomes a man, becomes an agent, proceed to become the bomber (the original that caused the most killings). at this point roberts can send ANY version of john (original bomber) to kill jane and thus the movie plot goes. (really roberts can manipulate anytime, w/c would make sense of the movie as he can now make use of jane/john as an agent because the person would be in limbo). well like you said it wouldn't make sense if she doesn't recognize that he is the one who fucked herself in the first place so i think originally it was a different man.

TLDR; I think roberts and his co. manipulated jane unto putting herself in limbo to be the perfect agent they needed (rob can go backwards/forwards and has authority over jane, unlimited possibilities on how we arrive to the movie conclusion). baby and jane cannot be the same person(chicken/egg thing) and she cannot be the original father (she cannot cause the original sex change herself, as she had to fuck herself first to actually be able fuck herself) the whole he/she is her own baby is the movie's biggest plothole and i just cannot come to a conclusion on how that could have been. (i.e best i thought of is that jane/john is tricked unto thinking so) movie's saving grace is that roberts can essentially keep moving back and forth in time, taking different versions of john/jane and manipulating, setting up the perfect scenario where we see the movie's conclusion.