Manga isn't necessarily canon. Manga are usually fan made and are kind of like myths to help explain something unexplainable, but that doesn't make them correct.
I guess a prequel wouldn't be impossible. It doesn't have to take place RIGHT BEFORE MM. It could be a game that takes place a long time before MM in Termina that explains the origins of Majora. It would be nice to have another Termina based game. However, I highly doubt it's a prequel to MM. My...