I agree with you that it is definitely not the best way, by far. However, of all the things I have seen installed on a roof, almost all of them have been installed this way. I think it also depends where you are and what kind of roof you have.

Most things that mount to the roof just drill straight though everything and then add waterproofing sealant at the top of the hole/fastener anyway

If only he gets jail… it’s seeming like that is probably not going to happen. I hope it does though.