I see.
The one at the school is the "bad" ending, as that means you failed to trigger the flags for the 3 characters. Nothing inherently bad about it story-wise though. The shrine is pretty much what I'd consider "canon" for this story, well, the extended ending of that route, actually.
Glad to know someone actually went to try the different routes though, especially since I've yet to figure out how New Game+ works. I'll make sure to have that feature in the future games.