crossdressing is not trans, you are ignoring people who do it for fun or some other reason and gender non conformists. The character identifies as his birth gender which means not trans. He does not seem to enjoy crossdressing either. Though with his aditude it seems like in some ways he wants to be more masculine and in other cases be more non-conforming. Or are you so ridged in gender roles that all girlish boys must be girls and all boyish girls must be boys. Even by definition Trans is about self identity.
She's not being a transphobe here, ootori is a boy and thinks like a boy, he's just forced to crossdress to fight and doesn't like doing it either
I'm being a little silly obviously, referring to him as she - but also it's quite clear there is a reasonable reading of Ootiro as an egg. You can see how he suppresses his feminine side in a very "I'm not allowed to do this but I still want to". He literally says "This form is cool but I can't show it to anyone". There's a clear distinction between Ootori and Haruno - both of them dress feminine when they get the choice to. Sometimes Ootori is just drawn like a tomboy, but Haruno out of her armor is always drawn feminine. Ootori is sometimes mistaken for a girl, too, or he was literally called "Barely a boy". These are all very transfem egg things.
I know there's a difference between crossdressing and being trans. Unfortunately, there aren't that many manga that are about being trans, so sometimes I read crossdressing/genderswap manga and headcanon them as trans. That's not bad, if you don't think being trans is bad - especially considering crossdressing is a way for some trans girls to experiment with their gender identity. You're right that he doesn't identify as a girl yet, though, but that doesn't mean I can't think that if given the option he will. It's okay to do either way!
Regardless, saying that dressing like that would make him a pervert is transphobic nonetheless. Because
she doesn't know whether or not he's trans.