... Hmmm... Well... This is just a random thought, okay? A random thought.
What if, in a moment of a breakdown, current twin Imouto told the class that "he" is a she and the students react like, "We already know! You told us that!" kinda thing... Now that's out of my system, onto the real manga.
The things you said (all the things you said, all the things you said [it's a song btw]) makes sense. About the Aniki-teacher having a relationship with the whole class... maybe the whole school but I'll focus on the class...
Maybe the guy only flirted and only went as far as kissing the gir--
Know what? I don't like the Aniki. Hope his plane crashes and he burns! MUAHAHAHHAH!!