If the issue was digestive acids then the inflammation wouldn't be localized. The acid is contained in the stomach, enzymes further breakdown the food and nutrients are removed in the small intestine and the large intestine removes water.
I have UC, so only inflammation in the colon. When in a flare inflammation in the colon starts at the rectum and heads up, and healing goes the opposite direction. If acid was the issue, the ulcerations would be along the entire length of the intestines starting at the top, and wouldn't be localized n the colon, my small intestine would be affected too.
Crohn's, on the other hand, can attack any part, including areas along the tract that prior to the stomach. Seeing as the esophagus and gums can be affected, and they only in rare and extreme cases of vomiting come into contact with stomach acid, the stomach acid theory doesn't seem to hold up.