Epoxy over paint can only stick and seal as well as the paint, which is far less than the epoxy can do on bare wood - so you don't want to paint first. Painting last, over the varnish is no problem as long as you sand the varnish where you want the paint to be before painting. Most enamel manufacturers want the surface sanded to somewhere in the 80-150 grit range to give the surface enough "tooth" for the paint to stick well.
You can also varnish over paint after scuff-sanding the paint but remember that varnish tends to yellow with age. Even with spray equipment it's quite difficult to get the varnish perfectly even. As it then ages over a solid opaque color, you may start to get an uneven, splotchy effect due to the varnish thickness variations (don't ask me how I know this). In any case, as long as the resin is cured (probably a week or more) and the paint or varnish used are allowed to dry for a few days before you add something on top of them, color-bleeding of any combination should not be a problem.
I suppose you could color the areas before glassing using pigmented epoxy, but it's a much more complex job than painting later. Most opaque resin pigments (including black, white and mixing powders like graphite or aluminum) take two or three thin coats minimum before they start looking even and truly opaque. I suspect that finishing the glass work, then varnishing the boat and finally lightly sanding, masking and applying a couple coats of enamel to the areas you want to cover would be the best way to go.
Without knowing exactly what you need to cover, would veneer strips or small "overlays" be a possibility? It's possible to buy very thin sheets of veneer from woodworking supply places like Woodcraft - real wood, sanded on both sides and only about as thick as a business card (not the iron-on or cloth-backed veneer strips from the big box stores). You can glue the veneer down to the bare plywood over the joints with epoxy or wood glue and then fiberglass right over it. The stuff is so thin that the level change will disappear in the fiberglassing, filler coats and final fairing stages. You do need a means of holding the veneer down tight and flat while the glue cures, but some handywrap, a scrap of plywood and some weights or clamps will usually do the trick. As long as the veneer winds up down tight to the surface of the ply it will actually strengthen the scarf as well.
I don't have any photos of a boat project done that way, but I built a mandolin for my brother a couple years ago and veneered the top with some super-thin curly maple, set in WEST epoxy resin and then top coated with more resin and varnished (didn't need the strength of fiberglass, so plain resin was used). The first photo shows the veneered and coated surface. The veneer was glued down, allowed to cure and then sanded smooth (random orbit, 100 grit) and epoxy coated. These resin filler coats were then sanded flat (photo#2). Finally, it got about fifteen coats of sprayed varnish which was later block-sanded up to 12,000 grit and buffed by hand (probably a bit much for boat varnish...) - photo#3
The veneer is reasonably cheap and kind of fun to work with. It might offer an opportunity to do more than just cover the scarfs.