I totally get your point. I had the same uneasiness in my memories of this tory, so I just reread it and I realized that it actually does solve these issues, in a rather subtle manner.
Well first, there is the fact that the first line of the whole story tells us that the first time he saw Yashiro cross-dressing Momose instantly recognized he was a man, which makes me believe that he never denies Yashiro's masculinity.
I feel that the final chapter is what's most revealing. Instead of having the obligatory "penetrative sex after they make up" scene Yashiro asks Momose to tell him he is cute (because he does want to be considered attractive by men) and then he asks him to touch him, which, in my opinion, serves to reaffirm his masculinity at a moment where them having pentrative sex would have simply feminized him. It does end with them sharing Yashiro's masculine fluids through hand-holding.
Also, when they do have sex in the bonus track and the movie special chapter (6.5 and 6.6) Yashiro is never cross-dressing.
I feel like Hideyoshiko has a real talent for writing simple stories with many layers of psychology to anlayse (when she's not purposefully delivering perplexing wacky material like Gakuen Tengoku).
This manga is realistic, with seemingly happy end.
And yet, it left me anxious for both characters in it.
This isn't a typical yaoi love tale - it is a story about conflict inside the characters, their confusion and uncertainty.
Maybe it's because of cross dressing I feel so uneasy after reading this manga.
It's just feels like Yashiro is in the very vulnerable position, and he might be needing rather some time to decide by himself about his sexuality and cross dressing preferences.
Momose is just as conflicted - it is difficult to understand him and his reasons. Although mangaka shows us some of his thoughts but the whole picture of his feelings (love?) is still unclear.
It would definitely help to see an acceptance of Yashiro by Momose by meeting each other without cross dressing. After all it's not like Yashiro is uncomfortable being a guy, he just likes to wear women clothes (and the reasons for that might be that he want to be considered cute, pretty and attractive by men). Therefore it would be painful to be in a relationship which is conditional on the cross dressing.
Sorry for such a long post - this manga stirred me up like nothing before