I think a lot of the pushback you see is coming at the idea that they're seeing you nude. Like, I've known people who don't want to wear the swimwear in the game because they don't want someone to see that much of them, and they aren't RPing when they say that. It comes across as a little weird.
I realize someone will ask "But the people modding for nudity aren't weird?"
To which I'd say no, not really. People are horny, and people express that in different ways. Mod scenes both SFW and NSFW have existed since the dawn of gaming and virtually every game you've played has a mod scene out there somewhere. Someone earlier in the thread mentioned The Sims which has an incredibly healthy NSFW mod scene that gets mainstream attention and from which some mod makers earn enough to live off of. Rule34 has also been mentioned in this thread, and if you talk to many artists and illustrators you'd be surprised at how many actively work in the NSFW scene because they make a ton of money doing it.
The point I'm getting at is that there's always going to be an appetite for this kind of content, and it's almost entirely self-fulfilling. Nobody is commissioning art or modding their game because they care about what you, the OP, myself, or anyone else looks like. The portion of those players who would then want to jeopardize not only the mods they enjoy but also their accounts by then harassing other users with those mods I'd imagine is insignificant enough for a thread like this to come across as pearl clutching. I guarantee this thread is not the first time Square-Enix has heard about a mod scene for FFXIV, and it's better business to let those players exist in peace than to crusade against them, provided they aren't rocking the boat much.
The better option is for players who DO feel harassed to either try to deal with Square-Enix directly to stop the person harassing them, or in the case of content hosted on third-party sites, to deal with the support staff of those sites if the person hosting the content using your character's likeness doesn't remove it at your request.
Late Edit: Personal opinion, but I'd almost be offended to hear they went after mod makers before they did anything to really clamp down on botting. The amount of gathering and PvP bots that keep on hanging out is a much bigger detriment than aesthetic modding.