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I had Yakama Cross bars on the aluminum hard top, and I sometimes carried two kayaks with saddles, and other times a canoe in the center and two bikes , (one on each side with Yakama bike racks)
Just make sure you mount the kayaks back far enough, so they don't come in contact with your tow vehicle on a tight turn.
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.
a camper manufacturing company, they might be a good source as some folks order their pop-ups with bike and boat carrying assemblies prior to shipment to the dealer.
Another option is if you see a set up at a campground talk to the owner and perhaps they'd have some feedback or allow you to check their rig out.