Why not just use a hitch mount, and keep from drilling into the hard cover. Keep in mind these are fiberglass covers and could start getting stress cracks from the vibration of wind buffeting along with chasis vibrations. Boats get them all the time.
I have an A.R.E whichare pretty thick and heavy painted to match the truck, and even though they have one as an option, I wouldn'tdo it. I use a Thule hitch mount.
I couldn't open the links above so I did a quick search on the sites. I used to frequent them, uhh frequently. I didn't find anything quickly but I know I have seen ways to mount roof racks on top of a hard toneau or a pop up camper. I really like roof racks over hitch racks especially on top of a tonneau because they are out of the way of getting backed into. However they are in the wind more, but on a tonneau, the bikes are partly blocked by the cab. Plus, if you are pulling a camper or other trailer, a hitch mount won't fly.