Autoimmune is one of several theories, I agree one which fits a bit. But as long as the autoimmune cannot be detected in any way it's not that the medical community isn't ready yet - there is simply no evidence, just a vague 'feeling'.
Like sunkacola I always have to be on my toes (pacing, treating) to keep my continual full flare down. Sometimes feels I'm OK, but only cos not too much triggers around and treating it well.
If PT is harming, say so immediately. If they don't adjust it, change quick. If it helps a bit and not harming, consider keeping at it a few months. If a PT listens to you and your body, that's OK. If they just tell you things and do things they always do for everyone, that's not. That's my experience of 15 physios (in fibro-times; plus 10 just for back before).