Just emailed backflip and they said exactly that.I highly doubt it'll fit with most tonneau covers as it doesn't just sit flush on top of the rails. Looks like it grips the sides.
There are several brands/varieties that will work with a Rambar. Watertight? No. But functional, yes. I have a RetraxPro XR and it works with the Rambar.I just installed a tonneau cover on my Rebel, with a RamBar. It is a PITA to do, and I went with a soft cover. The Mopar one wont work as it goes on the bed rails. You need to find one that has the tonneau rails on the inside of the bed, and remove the horizontal bolt from the RamBar. I will be tweaking mine for a while to make sure I get a good seal on it, but it is functional, and I can roll it to the front of the bed with some maneuvering.