I would be concerned about the potential of the rear bouncing. The strap that ties the frame to the front bracket helps but you can't tighten the strap to a point where it isn't elastic enough to allow movement. The tire pads reduce the force on the surface but does not hold the rear of the bike down. You could add weight to the rear of the bike but the bounce could still happen. My preference would be to find a way to hold frame down to the surface, the further back the better.
The only restraint keeping the bike from flopping on its side is the force of the QR on the front fork. There are two joints where the bike can rotate, the head tube and the front axle. Bouncing the rear wheel could cause the rear to move side to side with the rotation happening at the head tube and the front axle. A Tandem has a very long moment arm (lever) from the rear axle to the front. If the QR isn't tight enough, you will get movement and it may "rock" itself out of the bracket.
How big a deal is it to you to make holes in the roof of your popup?
Any roof rack could be mounted to the roof of the popup just as it is mounted to a car. Frankly the MPG is going to be about the same if it is on the trailer as if it is on the car roof since you are still sticking something up in the air.
If you wanted to get creative... you can get the basic fork mount clamp by itself for pickup bed mounting. Mount that on a chunk of square tubing and then mount the tubing to the popup. The tubing will provide a broader base to take the leverage/load from the fork mount. You could mount another square tube in back to take a strap to hole the rear wheel in place. Pretty easy stuff.
You do not really need the straps they show if you have a simple rear wheel strap.
Couple of good solutions! I like the SeaSucker. If the roof is clean and smooth enough to keep the suction, your are good to go. For long term solution the other would work well too. The top of the camper is likely fiberglass. Any item mounted to it should have some sizable base to distribute the load/stresses and minimize stress points or small high stress areas. Flex will happen if mounted away from edges or features, or another way to say it, mounting in the middle of a big flat area is to be avoided. Use large fender washers with the bolts and a good sealer around the holes on both sides. Having the front and back mounting connected with a stiff (structural geometry) piece of steel or aluminum would be good.
MPG will vary slightly if the bike does not stick up above the roof of the vehicle. It may not be measurable given the extra weight of the trailer. I don't like roof racks due to the whole driving into the garage risk. Don't know what other things might be targets on the road.
I'm not sure about putting holes in the roof! We'll have to chat to a few people about that.
I originally looked at mounting a roof rack onto the top of the camper and it wasn't recommended. The roof itself is easily warped with weight. There is a specific rack intended for pop ups and it has poor reviews. I was hoping that if the bike weight was more supported on the tongue of the camper itself it would eliminate compromising the roof.
Dont think we can swing the inner tube option either! Other than the tandem we will most likely be hauling 3 singles.