Canonicity is merely a term used to represent veracity with respect to author's intentions for the material. Female Main Character was put in specifically to provide another facet to the story. In other words, specifically to expand the "canon" material.

There is not "multiple canons". Canon is an inclusive term of everything that the writers believe contributes to the overall universe they are building.

Non-canon includes things like the Chie beef bowl brawl with Akihiko or Yukiko's lunch box obsession. Things never developed to be an actual part of the world, but just for fun.