I think it’s because they changed the story a little from the source material to more neatly fit it into the format they needed for Season 1. To some people familiar with the source material, that’s heresy and absolutely destroyed the story. As a fellow anime-only, however, I felt the story was perfectly fine as it was told and I’m looking forward to seeing where they take it next season.
After all, it’s not like they pulled a God of High School on us.
Nah, the final arc is huge, far too long for even a 2 cour season, and there’s still a mini arc before that to tie up a loose end from season 3. Plus, I doubt they’ve storyboarded any of the unreleased chapters yet. At a guess I’d expect this to be 13 eps, then a couple more years wait, then a 2-cour season and finally a tie-in movie to finish. That being said we still don’t know how many chapters remain so it could go on longer than that.