There are different types of fiberglass resin with the most common being polyester meant for bulk layup work that will be sealed by gel coats or paint so do not count on it being water proof or hard enough for a good top coat. Vinyl ester resin is a little more expensive but superior to polyester - I used VE on my plywood flooring with the 1st coats thinned with MEK. Epoxies are the best but will cost almost twice that of PE or VE resins.
But please don't blame the trunk for all the damage, every seam on endcap, all the gaskets on windows and utility hatch, tail lights, awning mounts, slow leaks on plumbing - they all contributed to the floor rot on my '73.
I am thinking about modifying the trunk also - expanded metal mesh floor and a true continuous barrier dropping from shell that wraps to beneath BW tank. Also, after noticing the bumper is just pinned on w/ 1/4" screws, I thought to make bumper flip-down or pull-out to eliminate the piano hinge and keep the trunk roof solid.
Also considering a marine inlet and detachable shore power cord; but having one end hard wired into trailer probably prevents opportunistic thievery...
The days are short and the night is long and the stars go tumbling by.. . ~Airstream~