To me it comes down to "canon but with X pasted on" (don't allow) vs "basically origfic with canon names pasted on" (allow sometimes). I wouldn't allow either of those Naruto endings unless they were demonstrably much more different from canon than those descriptions suggest but I might allow, say, Neon Genesis Evangelion: Angelic Days (although that's also not a great canon high school AU example because eventually the angels show up in that universe too). And, of course, where the yuletide mods draw the line is obviously going to be different!