Very nice car but it would be a shame to cut it to fit the flap!
It will rust no matter how you treat it IMHO. Different story if it's factory fitted.
It's only useful if you rally the car anyway so what's the point?

 

It wont rust if edges are painted, factory car has the roof skin cut so no any different if done correctly.
And its a great mod, the amount of air that you can get in to the cabin is worth the mod alone.