The scary thing is, iBeacon handler don't have to do the cute "hey you're in this store, click to open the app!" sort of thing. They can run completely in the background, just reporting "hey boss, they're in the shoe section of Store #3313 now! Now they're in the produce section! Now they're gone." And, as far as I know, there's no way to turn off the tracking behaviour while keeping the helpful "activation suggestion" behaviour.
I have no idea what APIs they use, so I'm not sure how hard it is to get this information, but it is at least possible.
https://github.com/transistorsoft/cordova-background-geoloca...
https://github.com/transistorsoft/react-native-background-ge...
Here I am driving around Iceland with my sample app, completely in background. Tracking engages automatically when device is detected to be moving.
It is fairly clear that there are no such heuristics in PoGo.
The reality is, Niantic is a small company, and does not have the resources to throw at detecting/banning/dealing with the appeals.