I just got this same message this week at ~8k miles. took it in to the dealer today and they said it's a faulty sensor, the part should be available in under a week and it's ok to drive in the meantime
I installed the roll-up cover mentioned in the original post with a factory spray-in bedliner. clamps work just fine for me!
mine is about 95% waterproof, just make sure to install the included seal on the front where the bed and cover meet