I do think that's the most likely intention, especially since Nekotofu's not made Mahiro trans even though we're up to 83+ chapters. Mahiro still thinks of himself internally as a boy, even though he's clearly enjoying being both a girl and underage again. (Like his happily asking for New Year's money from the families of his friends in chapter 83.)
I don't think that reading of Mahiro is really justified - Mahiro hasn't fundamentally changed, so the argument can definitely be made that there's been no change in gender identity, either . . . but taking that to mean Mahiro is clearly masculine presupposes that Mahiro was always cis-gendered, and there's no particularly strong reason to believe that (at this point). Yes, statistically speaking it may be a reasonable assumption, but looking at Mahiro as an individual I don't think it's necessarily a good one.
Mahiro was assigned male at birth, and clearly grew up accepting and internalising that, but at the same time it's pretty clear there was never any careful consideration behind it. Being genderbent
forced that consideration, but being genderbent
forcefully actually made that consideration harder, because it's natural to push back against being forced into something like that. But Mahiro adjusted pretty quickly - in fact, it ended up making very little difference early on, and it was only when social challenges came along that physical versus mental gender expression had any significance. Even then, Mahiro quickly got very comfortable with presenting as feminine . . . even though there's also still a definite tendency towards the old stereotypically masculine behaviour and patterns of thought. And I don't think you can say Mahiro has ever shown any particular discomfort with being
either a girl or a boy - it just doesn't seem to be that important. Given all that, at the moment I'd be inclined to say that non-binary would be the best description - neither one nor the other, with no clear preference, and a significant amount of fluidity. Maybe that will change, but for now I think it's really hard to say that there's a clear preference one way or another.
All that said, if you asked Mahiro right now "are you a girl or a boy?" I expect the answer would be "a
man!", and . . . . well, that's generally what matters most. But if instead you asked "would you prefer to keep living as a girl, or go back to your old life?" I think you might get a different response; at the very least I expect you'd get a long pause before getting a response, and I'd probably give fifty/fifty odds on which answer you'd get.
Which is a large part of why I think Mahiro's gender identity is mostly irrelevant, rather than being central to the story - the genderbending is there to break Mahiro's old life open, rather than as a specific challenge to anyone's gender identity, and the story is really about breaking out of the unhealthy mindset that was ruining Mahiro's life.
Minato's side story might end up being a
real consideration of gender identity, though, which would be a nice adjunct to the main story . . .