Something that has hopefully not been overlooked for the paid version - making sure there is an ability to restart from the control panel (or whatever) - after issuing the shutdown command as root I thought refreshing the page might attempt to bring it back up but alas I was locked out for the rest of the 15 minutes.
I'm not sure if this is how the specific ones being talked about might be working, but a simplified way of doing it would be that when APP A is installed it connects to a server and tells it that it has been installed with UNIQUE DEVICE ID, that way APP B can connect to the server and see if APP A has been installed on UNIQUE DEVICE ID. You can imagine ways to do the same with viewing ads etc.