Based on the posts/links so far, no one seems to know exactly what is causing the games to not be allowed aside from the developer(s). It seems to only be ambiguous phrases, but there is nothing else I can see. "Nintendo changing policies to stricter content regulations" or "Expression Restrictions" doesn't really say much either. It could be character related depictions, phrases that are used, etc. Or it's getting rejected for something else not even related to the usual stuff we would typically see modified?
Seems they aren't even releasing an edited version either, so we likely won't be able to see an original vs edited comparison. Only thing at this point is to wait for the PlayStation release and check out the content for anything that maybe would cause it to be rejected elsewhere. I don't play these specific games, but I still always find it interesting and annoying when there are regional differences/edits - so I always find it an interesting discussion (before the usual people come in to shit on the thread).
PlayStation has mostly been in the spotlight when differences are found, but Nintendo isn't necessarily immune either. We've seen regional differences for phrases and/or animations (too lewd?) from them from time to time (mostly on 1st party games, but there have been other releases modified too). It's typically inconsistent too. Which makes it even wilder when you compare it to what the other posters have said about the current state of the eShop - it doesn't look like they do much enforcement on content quality there. The previous iterations of these games have made it here physically too.
Overall though, I think we need more concrete proof of anything changing (Policies, Guidelines, Future Games, etc.). Otherwise, this sounds more like the random rejections Steam would do (which is also inconsistent).
**As for the upcoming Xenoblade X Definitive Edition - It'll likely be based on the version we got in America like Isa mentioned, so it'll include the edits of the original most likely. Similar to the Tokyo Mirage Sessions, they based the updated ones on the international release which was already modified.