It sounds like you tied the boat off to the craddle assemblies and not the rack bars. The best way to tie off is to go around the boat and down under the bar then back up and over the boat such that the caddle isn't the weak link. The nylon straps and the attachment to the vehicle are much stronger than the small bolts and plastic pieces of the craddle assembly. If you do this and the bow and stern you will have a 6 point attachment. You should also replace your nylon straps regularly. Don't worry about the boat it can be fixed without to much trouble.

The varnish is pretty tuff stuff sanding is about your only solution.

Kent