There's certainly a lot of ways food substances can interact with bodily systems. However it can be hard to discern the exact source as different substances are correlated. Like you mention, issues with FODMAP is common, and those are often correlated with carbs. So there's a significant risk that a real effect is misattributed. Ideally you'd test if by blinding the intake, but that's often impossible or at least infeasible, so in the end we tend to latch on to some hypothesis without too much evidence.

It's also good to be aware of how strong the nocebo effect can be in this context. If you are convinced of the danger of something it can lead to significant issues. For an extreme example, severe airborne peanut allergy seems to be hard to be reproduce in controlled studies, yet there's people having significant symptoms from this, like lack of breathing etc.

Basically, when it comes to food, a lot of skepticism, including to our own experience, is often required. The risk is that we otherwise end up with unnecessary restrictive eating.

Personally I have a lot of things I "can't" eat, but even then, I try to challenge it now and then, sometimes I find something in a category I can actually eat and sometimes it turns out that I can eat it in low amounts or slowly learn to handle it.

Maybe it’s not carbs, but something collocated with carbs like glyphosate.

Same. Other substances too. A couple days ago I switched from white wine to red at dinnertime and my fresh mosquito bites immediately started itching when before that I didn't notice them as much.

It's not hard to believe that immune responses (allergic reactions being one end of that spectrum) are affected by the body's response to ingested substances. Especially given how strongly the gut microbiota affect blood chemistry.

A friend of mine is very sensitive to histamines. Can't drink red at all, only special low histamine white wine.