Thank you ! I'm so happy you liked the game despite its flaws❤
To answer your questions :
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A lot of people were confuse as you were and even angry and for that I'm sorry. It was because I didn't handle the writing for his route as well as I wanted too and only realized it later with the feedback (u___u)
Haru is indeed biologically male, but although he doesn't feel the need to be female nor suffer of dysphoria, he does hold a certain grudge to adults and male in general due to his backstory and the toxic relationships his mother was in through his childhood, hence the "I don't want's to become and adult if it's to end up like all the men I knew in my life until then".
About the crossdressing part it's also due to his backstory, but also because even though he doesn't want to become "a man", he is also very self-conscious of his small size and frail stature for a boy his age as well as his androgynous and fill better about it and like wearing feminine clothes because he feels more safe in it.
And about Aya, she is actually saying that she felt for him when she thought Haru was a girl, but also means it would have been the same if he was a boy.
It's not really explicitely said in game, but Aya is pansexual so she would have loved him no matter what✦
And his answer was more like if he knew, he wouldn't have bothered to try fiting more on the "male" case and work more on his "himself" case.
In conclusion Haru is not trans, he simply feel better and secure in feminine clothes due to his physical traits and doesn't fit what society expect to him as a male.
I think you could say he is a non-conformist character and I'll try to portray him better in the remake ~
I hope it answered your question, if you have anything else to ask don't hesitate to tell me and I'll gladly answer (^ O^)/