I don't see a reason not to drill. If you prep the area before and after, it should be fine. People have been doing this for years in the RV and boat industry. It should hold up fine. In the event you want to plug up the holes later, you should be able to do that fairly easily with some fiberglass or epoxy.
I think having an awning
rail on there firmly with rivets or bolts would eliminate the worry of it pulling out while towing and having your bag awing turn into a hazard on the road.
The straps idea seems cool, but a project to set up and take down.