Some content just makes certain games harder to market in some regions than it does in others. Face rubbing in Fire Emblem Fates was completely inessential to the experience of playing the game (any bonuses derived from it are automatically given in the western release), but more to the point, it’s a mechanic that NOA felt enough people in the wes would find weird/skeevy that it was removed during the localization process.
As far as TMS goes, no actual features were removed in the localization. They altered one dungeon to be focused on fashion modeling instead of gravure idols (which is distinctly an adult industry), made some costume edits, and rewrote/recorded all of the relevant dialogue so that all of the changes fit. (Some people went so apeshit over these changes that they tried circulating faked screenshots that made it look like the localizers had no idea what they were doing, which is its own level of weird.) But nothing core to the game’s design, story, or themes were hurt in the shift.
And Xenoblade Chronicles X? OK, they took out a boob slider. It was a very innocuous change and I don’t know many people that agree with it, but it happened. But again, it’s not a vital component of the game.
Localization is a tricky thing. Sometimes changes are made to make a game easier to market, or to reduce potential for offense. Where the line between “just enough” and “too much” is really varies depending on what the game is and what’s been changed. I tend to prefer that where features are concerned that games remain in parity with the Japanese version, but I’m not going to throw a fit and scream censorship if face-rubbing is pulled out of a strategy RPG.
I’m more annoyed by localizations that try to swap out Japan for the U.S. (ex: Ace Attorney), which at best makes everything feel kind of weird and at worst is intellectually insulting or white-washing.