This manga is so timeless, I tear up every time I read it. ...I say that, but this was actually my first time rereading the story since I first read it back in 2021-22 and at the time I did not pick up on any of the trans theming at all. Coming back to this several years later and more mature than I was back then, it's incredible how much my view of the story changes from realizing Maya is trans.
Of course there's the "evidence", with her looking 'boyish' in high school, getting disowned by her family while 'studying abroad', her breast augmentation surgery, and the role she played in the theater (which I totally missed because I wasn't familiar with the play, thank you for pointing that out @Gabinomicon), the name Maya "not being used by many people", etc.
But on a far more fundamental level, Maya's entire character arc and her fears make a lot more sense in context of her being trans. Feeling like you are fundamentally worthless unless you can be useful to others, and that you'll be thrown away as soon as your use runs out, and the belief that your own desires and wishes are already guaranteed to be destroyed if you actually go after them. Running away and hurting herself because she thinks it's the only way to prevent other people from getting hurt. Feeling like you aren't the protagonist in your own life, and explicitly comparing yourself to kind helper characters like glinda the good witch because you can't imagine yourself as a human who's just as important as those around you.
All these aspects are things I've struggled with myself as a trans woman, and the context that Maya is trans makes everything about her character just click in such a way that it's impossible to see it as coincidental or unintentional. Of course she would try to erase herself from Yuuta's life and view herself only in terms of the liability she might present others, rather than going and trying to seize what she wants from life! She's been denied everything up to this point, whether it was school, her family, or even michiru in the past! The times she did do the things she wanted (ie transition) she lost her whole family! So of course she would have all these hang ups and try to repress her obvious feelings for Michiru, because if she acts on her desires again, she'll lose the new family that she's made! And of course, in the process of doing this she is actually pushing away that same family and resigning herself to a lifetime of repression and loneliness, while telling herself it's all for her family's (michiru and yuuta) sake!
The thematic resonance is too powerful to deny. What an incredible manga.