He seems, to me, to be comfortable in a male gender
I don’t think we have any textual evidence for that. For someone that age who is assigned male at birth, the fact that they live as male, especially in a more conservative society like Japan, is practically guaranteed, so it doesn’t tell us what their preferences are. And there’s nothing in text that suggests they are comfortable in that role.
In this latest chapter, Kouyou goes "I am Momiji" and "Kouyou is Momiji" when that first statement is denied. It feels as if she is correcting Konno and asserting that the personas are both her at the same time despite the switching presentation.
Being transgender and having DID are different things. This line affirms that the personas are the same person, which is true of people in general that aren’t plural. I think you might misunderstand what it means to be transgender: when transgender people transition and adopt a new name, they don’t conceptually create a new person with the new name that is distinct from the old person, but rather change the name and clarify the gender of the existing person. The fact that the two names refer to the same person is obviously true, and doesn’t necessarily have anything to do with being genderfluid.
I am expecting it to show a character who identifies with multiple genders and shifts around and between them (as I see it is currently doing)
But is that what it’s currently doing? Have we ever seen them make an active choice to present in a male way, beyond following the expectations assigned to them? That has not happened so far, and if it did happen, it would actually be a big character moment, and strongly imply genderfluidity. But until we see that, there’s not much in the text to support this.
In fact, if you ignore the lines where the character states that they prefer being a girl, you could formulate a much stronger case for the character being agender, because their choice of presentation is determined entirely by external factors – like what the school allows them to do, or what Ao likes – rather than their genuine preferences.
“Genderfluid” is not when you present as various different genders at different times because of varying social expectations. That’s just part of the human condition for many. Genderfluidity is when you make an active choice to present as the gender you want to be at some given time, regardless of what other people think. Until we see evidence that that’s what’s occurring here, insisting on genderfluidity only serves to misinform and mislead people about what it means to be transgender, and what the lived experience of transgender people is. I’m sure a lot of the transgender people who read this forum will relate to having to switch gender presentation depending on what people are around. This doesn’t make them any more genderfluid, it just means that they’re oppressed, and labelling this behaviour as somehow inherently relating to genderfluidity can dangerously shift away conversation from addressing real oppression. (Of course, this is just a manga, so it’s not nearly as important; I’m just explaining why I think this reading is rooted in harmful ideas.)
Really, I’d just like to emphasize that these endings are very different:
1. Momiji continues as is, with no committal to any particular gender. In this case, I think “transgender woman” is the best reading, with “they just like crossdressing” also being a good reading.
2. Momiji makes an explicit decision that they will sometimes present as male and sometimes present as female, regardless of external influence (like what the school expects, or what Ao wants). In this case, genderfluidity is accurate.
I think that confusion won't fully resolve itself until she comes to terms with finding both of them cute and Kouyou's boy side coming along will challenge her to follow through with resolving that confusion in some way.
I think that would be quite an unfortunate conclusion – very much leaning into the dykebreaking angle, even if it’s not as bad as it could be. I admit it’s likely, but I’m still optimistic, I suppose.