I literally scraped them off my Devon roof using a Stanley blade scraper and then painted it with rustoleum. They seemed quite deep seated so I had no choice in the end.
I got most of it off with hot water and jiff tbh, just the stubborn stuff with a blade. I was painting it anyway.
Barkeeper's Friend, the cleaning stuff will likely get them off. Will need a good waxing, or the mould will be back.
Gelcoat is pretty immune to chemicals. If it has gone chalky, a sanding with fine wet and dry then a waxing will help. Bleach, fibreglass cleaner (oxalic acid.. i think the Barkeepers Friend maybe that too) If you are getting mould under the cover that means its damp.. think about metal rotting under that cover too. Sometimes might be better having something UV proof as a cover but lighter and porous so it dries out quickly.
