Well, I left what I mean by "cleaning them up" mostly vague on purpose because I don't have a strong preference to how it would happen, I just wanted to express a preference for it happening at all.
If it were up to me (and it isn't) what I would envision would be an optional interaction/sidequest to fix up some showers that the enemies around the map could use. For example, the small safehouse that was a college residence directly west of syn-tech could be refurbished a bit and a sign put up to let the enemies know they can stop in and safely shower/rest/relax for a bit. I would keep it as a safe spot for the player under the watering hole principle or you could cut a deal with ariana to manage it. Or you could do something with the gym, since it presumably has some showers in the building. This would then switch the enemy sprites and dialogues from being covered in dirt/garbage to being clean. They'd still want to fuck you senseless of course, but especially the vagrant just looks like she needs a bath and a bed to tone down the crazy eyes a little bit.
But again it isn't up to me and exact implementation isn't really my worry. Just getting across general preferences/dislikes.
Also I'd like to push back against being hard set against fetish options a bit.
And I know "don't yuck other's yum" but by the same token you can't yum someone's yuck. The in game descriptions of the characters smelling bad conjures up thoughts of literal hot garbage and sewage water smell which is incredibly anti-sexy. I'm very grateful that the lab assistant and wandering schoolgirl don't have descriptions of smelling like rotting flesh because I probably would have quit playing before leaving the starting area (and I tend to avoid the undead anyways because of the imagery of having bits of flesh missing. The poltergiest and frankenstien are great though!). Options for stuff that will really get a lot of people turned away can be useful.
Can you go overboard with them? Sure, and if toggles like that are added (which, again, I'm not asking for but it is a potential solution) you do eventually have to draw the line somewhere and it will feel arbitrary no matter what. But options and toggles are a tool, you just have to use them appropriately.