There are several factors. First, acids are only one kind of chemical that can cause irritation. Different chemicals can cause different kinds of reactions with tissue. Something that triggers an allergic reaction, something that weakens the mucosa, and so on.
Stomach acid alone is quite strong, but once you add food and drink, it gets diluted. The stomach isn’t constantly filled with lots of strong acid, it starts producing more acid in response to eating, and the acid quickly mixes with the food. As the acid reacts with the food it is partly neutralized.
Also, many foods that cause problems for people actually kick in when the stuff moves past the stomach and into the intestines.
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