Thule xporter rack mounted with tonneau?

So was wondering if anyone has figured out how to do this, I just picked up a nice rack, it mounts to the bed rails. And the tonneau runs the length of the bedrails.... has anyone cut their tonneau rails to size? Also This rack has the height adjustment, but with our wheel wells running the whole length of the bed you can't drop it. I am thinking of cutting the rack to the size it needs to be and fabricating some kind of sleeve to run it out to full length. I am posting this to get thoughts.

I want to run this thule rack at bed height in the winter for when I put my box on. I am thinking it will get a little bit better gas mileage. But I don't want to have to sacrifice eliminating my tonneau to do so.

Thanks for any input!