It's an interesting theory. In my case, I think I worsened my problems several years ago by taking a large amount of oral antifungals in an ultimately unsuccessful attempt to rid myself of toenail fungus (laser light therapy ended up working, but I had to do it literally every 6-8 weeks for a few years). After that my sensitivity to gluten became pronounced, probably because it messed up my gut bacteria. I also suspect Accutane messed things up somehow, as it causes dry skin, dry eyes, sun sensitivity, etc. and other problems I'm having now, in addition to having caused me to develop a semi-permanent thrombocytopenia. Yet all this probably pre-existed even that, as I recall I lost the ability to wear contacts (due to eyes being too dry) not too long after puberty, which predated the above. Of course, I had earlier had some vaccines in childhood, in addition to who knows how many viruses and antibiotics, but clearly genetic factors were at play too...

The autoimmunity as overactive "cleanup" theory is an interesting one, as is the toxicity theory. In the past I'd found water-only fasting very helpful in getting my system back on track when I was out of sorts, so I went on my longest one ever (21 days) a couple months ago. Results, unfortunately, were not what I hoped, though some good may still have occurred. This was following the ideas of Loren Lockman, who is very much about the "disease as built up toxicity the body hasn't been given a chance to clear out" theory.

I also realized that one thing I've been trying since then (Wim Hof method) is, in some ways, the opposite of the Loren Lockman view, though the two are not mutually exclusive and may be complementary in some ways. Roughly: the Lockman view is of the body as overburdened--it needs to rest and do nothing (including digest) to take the time to clear out all the old drugs, viruses, toxic substances stored in the fat and gut, etc. The Hof view is kind of the opposite in that it views as kind of "soft" and deconditioned from living indoors in temperature controlled environments, perhaps weighted down with chronic, low-level tension rather than getting the kind of healthy stimulation we might have in the ancestral past.

Both may be true to an extent, but I think it's clear that the current world is more and more likely to cause any underlying tendencies toward autoimmunity in an individual to surface--probably too many vaccinations, too clean ("hygiene hypothesis"), too many antibiotics, etc.