This is still one of the silliest non-issues I've ever seen. Besides the minor clothing edits, the one story-edit was chapter specific and was obviously done to decrease the age rating: Not only due to the characters being aged up, but due to it being T when the OG trailer from the first reveal in the US stated it was expected to be rated Mature. Considering how the Japanese release was a B, it's more or less clear the edit was done to make it T rated for the US and fit more with the same age range that the original release was going for, and not to increase it due to the ESRB's ruleset. That and 2016 Nintendo wanting to do literally *anything* to make games more marketable for their dying Wii U, since it's clear they're a bit more loose with edits now and only do them when it's an absolute *must* instead of as a precaution.
It's also not uncommon for the "International" versions of things to be made the new master version come a rerelease in Japan, like in the case of encore. Acting as if the minor edits and the weird story bit is what kills the entire game, from the whole main plot, the characters, the battle system and side quests is just utterly stupid. I find the cutting of the hot spring DLC more of a "problem" than this and I just find the DLC cut more annoying for having less things to do and them not bothering to edit if they needed to,, rather than a crime. The original devs are OK with these changes, localizations make these kinds of edits all the time in the form of text being toned down or altered. (sometimes too far for the sake of being silly, like in Snack World's recent mess of a localization)
The Yakuza games had stuff tweaked and altered in their remasters. Especially 3 which had a pretty not-nice sidequest that the devs decided to replace and remove due to the times changing.
Xenoblade is dubtitled to hell and back. (the JP audio's the same, but the subs don't match any of the things being said at all and all the stuff about gods and whatnot are just ignored, and as someone who knows a decent bit of Japanese it's really obvious hearing someone say "Kami", the word for god, but no mention of god whatsoever.)
Heck, even Pokemon isn't immune: Super Mystery Dungeon has a segment where the main characters are literally banished to what's practically Hell (being a world of emptiness and misery), and the Japanese dialogue and dungeon names at that point in the story represent this by labelling one dungeon "Hell Badlands" and using forms of the word Hell/nothingness a lot. Yet the US version renamed it "Voidlands", named the dungeon "Abyssal Badlands", and did all that for the same reason TMS toned down the fashion dungeon, to keep a similar rating to the JP original and to prevent SMD from going from an E rating to an E10/T one.
You didn't see anyone complain about censorship or the intensity of the situation being lost a bit as a result with mystery dungeon, because barely anyone who ends up bitching about this sort of stuff can hardly read the original text behind it to begin with, and thus none of those reactionary sites or channels made a point to label it as censorship, when by the definitions people seem to like using, Super MD was doing just that. I guess because it doesn't have breasts or fashion involved, or it's not a visual edit that bypasses language barriers, people don't seem to care too much.
But TMS is a seriously great game and however you choose to play it, I can't recommend it enough: They could have easily made it low effort and dubtitle the whole game but they did a darn good job at keeping the text as consistent with the dialogue as possible, and the rerelease makes it a far more engaging experience to play. It's a shame some people are passing on it or continue to ignore it over these edits, even though they're the least concerning aspects of the game by far. Go bug Snack World for silly edits, not this game. Of course, this is also a metacritic fault in general, since we know this is a trend lately to just hardcore review bomb titles for the heck of it, and I believe some indies like Kunai have been struck unfairly over it too, but I'm not surprised to see the old discourse back again
TLDR: TMS is a great game, ignore the bombing, go play it if you like good RPG stories