@smolbaka
"Did something happen in her early life (that we don't know of yet) that caused this fear of men?
Knowing your best friend looks like a girl but is in reality a male couldve made her feelings more confused.
Like she's lying to herself because deep down she does like him but since he's not the fitting image of what a boy should be it'll be weird to admit she has a thing for girly boys.
Plus the fact he doesn't even understand his own feelings of his body which adds to her confusion."
I think you misread something somewhere. Kotone is a closeted lesbian, and she quietly grew resentful of men because of that. Her current mood is because of guilt and frustration at not being able to love Mogumo regardless of gender (she deep down thinks of Mogumo as a male), not being able to accept Mogumo's gender identity (nonbinary - neither female nor male), and being born a lesbian (and the fear she'll be forever alone because of that).
She absolutely does not like girly boys. She doesn't differentiate between them and other guys. As a matter of fact, she seems to be a little disgusted with them. She's a girly girl who likes girly girls.