Hey Rob; you likely are already aware that there are pitfalls in the compatibility of polyester resins (fibreglass) and most epoxies. Please confirm with your supplier that you have compatible products!
We had a conversation earlier about S1...it for sure is safe to use under polyester.
The other potential problem down the road is 'contaminating the surface with varnish; that'll be a nightmare should you ever need to do a fibreglass repair!
I'm under the impression that acrylic coatings are the preferred protective coating : FIBERGLASS PROTECTIVE COATING : Rainbow Tech
Another component in polymer paints is the binder.
Binders are the chemical compounds that cause the pigment particles to bind to each other. The binder is typically a plastic including resins such as acrylics, polyurethanes, polyesters, melamine resins, epoxy, or oil.
All of the coatings above work well with metal or wood. Only the bold faced types (above) work well on fiberglass.
FRP is different because of it's typical uses of Fiberglass (FRP) and the additional protection specific types of FRP require. Oil, melamine, and acrylics have too many disadvantages to be effecively used on FRP. How to Paint Fiberglass
"Paints for FRP should not be oil based and melamine is not durable enough, to make a good coating. Acrylics, polyurethanes, polyesters, and epoxy are best. Note that the pigment in epoxy paint protects it from ultraviolet light. In matter of fact the worst thing for epoxy is direct exposure to sunlight without some sort of protective coating."
Being as how the boat's clearcoated, UV protection is the objective of any top coating.