I can see how you arrive at that conclusion, but it’s one sketchy paper, and they make no mention of types of bacteria and if or not the higher levels actually had a causative effect. I don’t think the link you make is valid at this point in time and with such limited information as there are completely conflicting results between Bart and Feldman that you posted. Feldman says levels are 1/10th in a healthy aquarium than that of natural reefs.I believe so.
well its all about pelagic bacteria. How much is good/bad? The Petcha.com article says ""More work needs to be done, but preliminary data suggest that in general natural coral reefs have lower bacteria levels than most reef aquariums. More importantly, healthy reef aquariums seem to have a lower bacteria level than unhealthy reef aquariums."
if "any stress on a coral, whether it be temperature or pH related, or due to any other cause, increases pathogens/virulent bacteria" then reducing bacteria, using whatever method is a positive.
However I think more filters feeders and diversity in our tanks can only be a good thing...