-- Last Updated: Mar-08-13 3:04 PM EST --
On my company work trucks, I've always had to mount a thick steel plate to the roof of the aluminum topper so I'd have a place to mount a magnetic flashing light. I just smear some silicone sealant on the contact surface and bolt it down, using strips of steel on the underside through which to run the clamping bolts. I found out by accident, when trying to transfer the steel plate from an old truck to a new one, that it can't be done. The adhesion of the sealant is far stronger than the aluminum. I certainly never had any leaks.
If one were to mount crossbars this way, you'd ideally put the cross-bar mounts directly over whatever framework is present below the aluminum skin, perhaps even drilling into those frame sections or devising a clamping method to enclose them within your improvised mounting hardware (the second option would be stronger, but that might be over-kill). This should be an easy project for someone who's done some metal fabricating, perhaps not so for someone who hasn't. I'd be surprised if Thule/Yakima haven't come up with a pickup-topper solution that would work fine on a pop-up camper.