Bought a 2017 Ford Raptor, with a BAK Cover. Are repairs to the cover, covered?

Hello - first, no one in this forum can speak to what is and is not covered by your MaxCare contract. The concern needs to be diagnosed, then the failure needs to be run by the contract terms to see if it is or is not covered. I would say, though, that since the cover is an aftermarket installed product and was not provided by Ford at the time of build, that it is unlikely to have warranty coverage.