Dmax - I also have a Reese Elite with underbed mounts. I had noise (clunk) starting and stopping. Figured out it was due to about 1/8" play where the top cradle mounts to the shaft of the base allowing it to slide forward on a stop and back on a start. And since it is all welded, no way to take up the slack. I bought a round flat plastic electrical box cover at Lowe's, drilled a hole in the center slightly smaller than the shaft, cut out one side again slightly smaller than the shaft so that it was in the shape of a C, and pushed it down on the shaft behind the cradle. Eliminated almost all the stopping/starting clunk. You can see the blue plastic cover in the photo below.
I had a bed rug on a 2004 F250 with a hard fiberglass tonneau cover before I had a 5er and really liked it. The hard cover keep it dry. But I was concerned about retaining moisture under it after a rain with the 5er so I went with a spray in. But the Reese does not ride any harder with this setup than it did with my previous 2007 F350 with a Pullrite Super 5th. I do have a 5th Airborne pin box though.