I find it fundamentally odd that the character who is advocating lgbt representation and acceptance in this manga is also a pedophile.
What's odd about that? If you think it's odd, you are viewing the characters not as people but as representatives of ideologies. A hetero, bi, homosexual, or trans person are all just humans with all the possible flaws a human might have. Being gay, for example, doesn't prevent one from becoming a criminal or have moral standards differing from what modern ethics would dictate as the correct ones. Not to mention in the distant past, also in the West, simply being homosexual could have been a crime, so that was the ethics of that time.
Psychologically thinking if Asako has lived a difficult life, under repression, she could easily be sensitive to the needs of other people. That's why she could recognise senpai for what he was. There was nothing wrong about that. Encouraging the vastly immature sexuality of a little kid like Masa is another thing entirely, but just like Asako was sensitive to Fujimura's troubles, she could also easily see Masa's desires. It was her flaw to go along with it, but humans can be flawed. Representatives of ideologies aren't flawed, by why would she be one?