If they used that program, then it resets the activation stuff on his PC so it thinks he is registered, and its already possible to install win 10 without a licence so he may never have know he had no key until if MS decides in the future to act on all the people running Win 10 unactivated. I would think they would have a way to know.
If that is the case, they charged him for Win 10 and got it for free themselves.