I can't remember exactly where, but I seem to recall reading that Jousei Shounan is around the point where the animators caught up with and then went ahead of the manga. While there was still communication between Konomi and the animators, Konomi wanted to draw his own story instead of just producing a black-and-white version of what was already animated ... which is why the matches between manga/anime differ although you have mostly the same schools (Rokkaku, Rikkai, etc.).