It's sort of an old joke, for at least the last 35 years, that PADI stands for Pay Another Dollar In. Their way of going to market seems to not miss an opportunity to add a fee anywhere there is an opportunity to do so. This leaves a bad taste in many mouths. It is probably one of the main reasons why several shops I have been to, that have PADI certification as well as others available, will often recommend that you choose someone other than PADI for your agency.
There are plenty of other options out there these days, but as long as PADI remains the largest &/or most well recognized, they will continue to maintain a foothold in the market. I think that they understand this very well & I think that this is a reason why they try to strong arm shops into being PADI only. It would be very good for them if the competition was no longer around or at least was marginalized.
That aside, I have yet to see a shop refuse to sell gear or fill a tank for someone with a SSI, NAUI, BSAC, or other type of non-PADI cert.
The last cert that I got from PADI was followed up by them sending me a questionnaire where they really grilled my instructor's performance. He is one of the people that can offer certs from different agencies. I am curious if that may be one of the reasons why they chose to put the heat on him as heavily as they did. By the way, I thought that particular instructor was fairly fantastic. He didn't deserve a grilling like that. He was one of the good ones.
This whole "self regulating industry" thing seems to be a very thin line away from corruption, price fixing, & collusion. That is not a knock on PADI in particular, that is a comment about the industry as a whole. The lawyers seem to be used as a political tool by those in the industry that are targeting larger market share. "getting investigated" is a good example of political pressure.
He probably pissed off a student enough that they mad some complaint that got PADI's attention and they investigated. That happened to me around 1992, one student in a class complained because she was mad that I would not let her buddy with her boyfriend during the class and she actually had to show that she could complete all of the skills properly. I even took extra time with her without charging her extra for it. All of the other students in the class refuted her complaint including her boyfriend and it was closed. PADI will investigate if they get a safety related complaint, the liability could cost them a lot of money if they don't. I also had a friend that I had assisted in several classes that was investigated and had to submit a statement that he had taught all of the proper skills in a class that I was assisting on after a student filed a safety complaint.