Yes, it's possible that excessively low pH could result in additional plant gunk from degradation of other molecules in the plant. However, some of these degradation products
may end up in the NPS or react with the alkaloids, impacting purity, yield or both. The alkaloids themselves will be unaffected by the acid (depending on the exact alkaloid of course, but DMT will be robust), and dilute phosphoric acid is not especially harsh by any stretch.
One further downside of adding too much acid is that it's simply a waste of materials - both the acid and the extra alkali you'd need to use in order to neutralise it. Phosphoric acid is not the cheapest of acids.
“There is a way of manipulating matter and energy so as to produce what modern scientists call 'a field of force'. The field acts on the observer and puts him in a privileged position vis-à-vis the universe. From this position he has access to the realities which are ordinarily hidden from us by time and space, matter and energy. This is what we call the Great Work."
― Jacques Bergier, quoting Fulcanelli