I am indeed, i know allergies vs non-allergies. Consider the reactions people have to fried food. You would bin that all under allergies with your logic.
Allergy is defined as an anomalous auto-immune reaction to an introduced substance. Indigestion from a common foodstuff is a good candidate. You would of course need a medical examination to reliably determine that your particular intolerance is allergy. But that's the way to bet.
Definitely not the way to bet since most reactions to food are not allergic in nature. Gut reactions should constitute the majority.
You miss "anomalous". I.e., it does not happen to almost all other people who eat identically the same stuff. Indigestion and diarrhea are common responses to dietary allergens. Thus, onions make my sinuses bleed and cause indigestion.
For myself, I get tiny blisters on the backs of my hands and neck from cranberries. And, onions make my sinuses bleed. Indigestion is more common.