We think it's basically on a case-by-case basis...is Friendship is Witchcraft a series with an ongoing plot, that would differentiate the canonical AU Pinkie Pie from the original? Or is it mostly just crack jokes and things that don't follow much of a storyline? If it's something with an ongoing, coherent storyline separate from the main storyline, and with different enough characters (as in the Doctor Who AU or YGO Abridged) then that would count it as a canonical AU here.