Concur regarding trait/profession differential; IMO all the positive-point professions could be redefined as Traits. No reason a wheelchair-user can’t also work in an office. Same with Drug Addicts (well, at least for a while, depending on the drug), etc.
If by “skill comprehension penalty” you mean “learning skills slower (or faster, depending on the trait/profession)”, yeah, I can agree with that, and support its use more broadly. Professions with a skill-book certainly ought to be able to assimilate it faster.
Sensory issues vary w i d e l y between individual autistics, so one fixed bonus/penalty seems inappropriate. Picking a problem a’la Martial Arts Training, might work.
Can’t speak for your girlfriend; I’m not her. (Speaks well of your taste in significant others, though.) I’m not synesthetic, so here’s a brief personal perspective: I can’t abide tobacco smoke or coffee shops. Smoke tiles would probably penalize as one density worse, as a quick estimate (I’d need to look at the code to confirm). Very Smelly NPCs may or may not be an issue: encountering one would be OK but rooming/sharing living space with one for a week was not.
Noises depend on what kind of noise and whether I can tell it’s coming. Practical example: I would probably gain morale in a Thunder Storm. One of my colleagues hates that horrid weather, though, and I watched her curl up in a safe corner to get away from the Crashing Boom Bang attacks. Our systems are wired differently, and that’s no reflection on either of us.
Clothing/textures can be an issue. I’d never wear Shorts, for instance, because I don’t like the idea of going around with my legs uncovered. (Especially if I’m going through windows/shrubs/underbrush/mutated poppy flowers/etc. Yikes!) Someone else might despise scratchy clothing like Dress Shirts. A third might have a favorite Peacoat and have morale problems if they take it out of inventory for more than (say) a minute or two. (Unequiping fails: might be changing clothes or otherwise safely retaining control of the coat.)
There’s something to that pressure & squeeze stuff. I don’t mind lifting weights, and have been asked to simply press on one of my colleagues so as to help him feel better at a stressful time. (Carrying weight over 50% of max-load would give a morale bonus?)
And lest anyone doubt my diagnosis, look at that wall o’ text. Autie carrying on and on and on here!
Bottom line: Autism, and certainly its sensory issues, resists being easily simulated in-game.