These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Everyone Is Jesus in Purgatory: There are legitimate reasons to consider it to be taking place in purgatory in this case.
Fanon: Yoshitoshi ABe purposely left a lot of the series unexplained, so that people could develop their own theories about the characters and about the world in which the story takes place.
Mado of Stone Mill is generally considered by much of the English-speaking fandom to be so well integrated with the main series that it is practically Deuterocanon.