Hopefully the top rail wont have to be trimmed to fit those tubular rails like these-
Is that the only part that requires drilling?
You'd have to modify the rails to fit those arms since it 1/2 covers the rear stake pockets. There's also 2 strips that attach on either side of the box that you clamp to because the box is tapered and the cover is square. It's pretty dry, but I don't know if it's bedrug dry. You'd probably want a cover that goes over the outside edges if that's the route you want to go as I do get a bit of moisture through the outside of the rails. Not much, but maybe enough to give you a mildew problem long term with the carpet. Did you notice the custom tie down rails I welded up that wrap over the wheel wells on both sides and are tied into the floor and under the lip of the box. It makes a lot of tie down points and also in my case a good place to lock bikes to. They weren't too complicated to make.
And they still clear my bed extender.