I will say that it's possible that removing a food for too long can result in a lack of the bacteria that help digest those foods. So, you can get a perceived "intolerance" to a food that you didn't have before by not eating it enough, but the reality is that you just have less of the bacteria needed to digest it. It probably takes a long time for that to happen though.
On a related note, some recent research shows that a peanut allergy can be cured by slowly and gradually increasing the dose of peanut in patients. This is analogous to Chris Kresser's opinion on lactose-intolerance: almost nobody is lactose-intolerant, if you start small and slowly build it up you'll be able to tolerate it over time (funnily enough, Tim Ferriss had proclaimed this years ago in a post on gaining muscle mass).
So, could most 'intolerances' be cured by just slowly adding it in? I don't think this would work in cases of SIBO, as you're feeding the wrong bacteria (the one in your small intestines instead of in the colon).