I like it better in the low position. When traveling at high speed.....there is no wind buffeting the rooftop tent....much more streamlined and better fuel mileage.
I bolted two pieces of one-inch channel to each end of the lid. This keeps it stiff and rigid. The tent is then bolted to the lid. I had to grind the small tab off the tailgate so I could open and close the tailgate. It might affect the "waterproof-ness" but it was never waterproof in the first place. I keep all my gear in two Zarges cases inside the mule. They are waterproof.
Hope this helps.