I was under the impression that polyester resin doesn't adhere to wood very well. If this is not the case what is the advantage of using epoxy on a kayak.

Personally, I would stick with the epoxy and use a good quality paint on the tonneau cover. Black looks good on them.

Epoxy doesn't start to breakdown until the temperature reachs about 240F, so you shouldn't have to worry about it. As it was pointed out before your interior plastics will be on the floor long before this.

Ian