When Kanji first realized he was attracted to Naoto he thought SHE was a guy. That didn't change his feelings toward her appearance and not due to "pheromones" it was a purely physical attraction based on her appearance. He did not think she was a tom boy, he thought she was a boy and was attracted to "him"
Now I would say Kanji is bi at least since his attraction toward Naoto is regardless of gender. He would have been attracted to her even if she was a he.
Ah gamefaqs, my home. The PS4 board is a nightmare.