Malabsorption is really a big factor with proton pump inhibitors.

They affect zinc, iron, (are you anemic?), magnesium, folate (methylfolate because of the MTHFR), methylB12, and perhaps other + and ++ions like copper, etc.

Glutamine is very helpful for some people. You'd need at least a gram a day. This might heal your intestinal wall. I'd suggest
going gluten free also. Gluten can inflame the intestional wall and cause malabsorption. Watch out for too much zinc... as too much may create neuropathy all by itself. Bluesfan was poisoned with zinc by her doctor! Some is okay, but too much is problematic. This can easily be tested for --get a zinc/copper ratio... as they are partners and need to be watched.

Make sure you take the methylB12 on an empty stomach for best absorption.

Doctors' attitudes towards nutrients depends on when they were in medical school, and where. This was just not taught in the past and some current schools still don't educate doctors properly.
Attitudes persist about using drugs willy nilly too by patients who want an easy solution. Got some heartburn? Take a PPi forever for it is the lazy solution, sadly.

PPis also inhibit absorption of protein (amino acids). Low protein levels then may create malabsorption of amino acids which repair the GI tract.