Once again, if the dive shop itself is not affiliated with an agency, what good does it do to report it to an agency? Even if the shop is agency affiliated, what is going to happen to it? The worst is the agency drops it so it is no longer affiliated. So what? It can still have agency-affiliated instructors working for it. It can still tell those instructors to do it the way they want it done, agency standards be damned.
The very worst standards violation I ever saw was more than 20 years ago in Fiji, before I even thought of being an instructor. On our first two days of diving, our group had a single diver who was obviously a real beginner. On each dive he did, he ran low on air early and was sent to the surface on his own by the DM. During the surface interval on the second day, he overate and opted not to do the dive. When we got back to the dock, he was greeted by a man who it turned out was his OW instructor. Those four dives, including the one he didn't do and on which he never performed a single skill, were his four certification dives! I wrote to PADI, and I got a reply explaining that the dive shop itself had no affiliation with PADI, so there was nothing they could do about it. They could only discipline the instructor. So the shop lost an instructor. No problem. Time to get another one.