Marinetex is stronger than polyester and takes drilling/threading well but is epoxy based. Blending gelcoat well requires patience and a bit of skill with progressively fine grades of wet sandpaper, up to 1000-grit.

If you were going to replace the snaps with other hardware I'd say fill and re-bore with Marinetex, but if removing it polyester/gelcoat is better. You can buy syringes for epoxy at WM (marketed by West System) that can also be used with Polyester, to fill the old holes. If they're full of old sealant you should bore them out first to get a clean edge.