The tonneau I had came with the truck, lots of dealers used to lower or lift trucks, then you just bought it with full warranty.
It was PIA when I first bought it, the lowering kit on the truck just did not work as advertised, ending up having to have the back half of the transmission housing replaced (tail shaft area), it would vibrate and bottom out so bad, it cracked.
I finally ended up getting the driveline shimmed (shims under the leaf pack, rotating the axle), replacing the drop shackles with factory ones (just a static drop), and having the wheels rebalanced. After all that, I still had a rough 3-5 drop, never bottomed out, or vibrated again. Could tow and put a normal amount of weight in the bed.
Good luck, the problems are hard to find when you alter the factory specs (geometry) of the suspension.