That's weird - I went to the Gem site and can't find any scuppers. Google brings me a page that when I click on it, it's blank on their site.
I'm going with the Gemlux 845s on my CCP too. They're beasts. Will your scuppers be oval too? I thin k it's a good idea to shim out the flap to plum; may as well let gravity work with you. You may want to try using the silicone and the stock flap together. That way, the softer silicone will help with the seal, and the stiffer rubber will keep things flat.
If the flap is too flexible, it could buckle. Why not try the stock scupper flap, and solve the problems as they come up. Bottom line, your boat your rules, so ether way, please tell us your results.