Love is not about what you deserve. It's about what you feel for another person and what they feel for you. You don't need to "earn" the right to be in love and express that love. It's sort of a central theme of the entire manga lol. And god what an incredibly good manga it is.
wrt the trans theories, I think it's intentionally written as ambiguous on the part of the author, and personally the trans explanation for Maya's motivations and changes makes the most sense. She was very butch presenting in high school, and over time as we see her in different points of her life in the various short little flashback snippets we see, she gets more and more feminine. If she was a cis woman, this change in appearance would perfectly align with her boxing herself up and molding herself for social expectations to avoid being hurt, rather than her personal desires for how she wants to be. However, if that were the case, she'd be back to being butch in the epilogue, where she's decided to be who she wants to be rather than what society expects she should be. Instead she's more femme than ever. Maya being trans just fits so well with the things she experiences, the things she feels, and the framing of a bunch of things in her life that are left far more vague than Michiru's past is.
Also a bunch of smaller details rather than overarching character analysis: 1) She's flat chested in high school and in the story's present has the biggest bust out of any character in the manga 2) That extremely important high school memory with the Prez is about playing Viola from 12th Night, a girl who has to pretend to be a boy but gets to transform into her true self as a girl at the end. That's a super clear metaphor lol. 3) In between when we last see her as flat chested and a few years later when she's not, she was "overseas" for some time, during which time her parents disowned her by removing her name (the one those parents gave her) from the family registry.
All of this is potentially deniable. But I don't know why anyone would be particularly motivated to bother when it's a better story when all these pieces fit together rather than just being random haphazard details. :P