Enzymes in general bring great benefit and your doctor likely has different opinions vs. my doctor about enzymes and safety. All I know is that I have taken pro-gest 2+ years now and its worked quite well. I basically don’t really need it anymore because my digestion has improved so much. I still think they work quite well though. I do think people should look into rotating them but I think they are quite safe.
As far as enzymes acting as prebiotics, I don’t think it quite works that way because they don’t contain many prebiotics from my knowledge. However, in general, it should promote beneficial cellular growth via the actions it performs in the gut (namely breaking down the food you eat).
Enzymes break down the biofilms that protect the yeast and when combined with SF722 they become a pretty potent combination.