You have reminded me of one of the other big mysteries regarding Maya: Who are her parents and why doesn't the school have any records on them or her? Normal teenage girl my ass.
Well, we know that she is not a child of the clockwork, but one of circumstance. So the chances are much higher that she existed outside of the supernatural stuff.
We also know that she met Akira after running away from home (following sexual abuse from a relative/family friend that was most likely not her parents), and then she moved in with him (at the tutoring place) after he bought her coffee.
We also know that she was the one that initiated their sexual/romantic relationship (green scarf), although it seems that he may have intended that from the start (pet the cat).
Then she forced him (which is a big mystery as to how and probably it was drastic) to choose between her and his past (to protect him from Sekai's memories), which made him cut all ties with Noriko and presumably keep renting a place just for her (?), until she got into school. Also, for some reason she seemed to start working at the temple during this period.
Couple of issues are: if it wasn't her parents that abused her, she was at least neglected enough that she felt she wouldn't be safe with them, and would rather stay with a complete stranger. Also, even if that was the case, Maya would have been reported as missing and would hardly be able to enroll in a school without alerting the police - unless her name isn't even Maya Makinami, which is a plausible assumption.
Anyway, she has a whole bunch of masks and I hope New Maya continues to leak a couple of what those are for us.
Unrelated: but I'm still pretty sure she got pregnant during the cycles because she's too adamant for that being the reason Ayane reaches the rooftop.
