I have seen a lot of painted ones, they usually chip over time but still are less visible than unpainted ones.
Another idea would be to not use the rivet-on "self-ejecting" style and just get the aluminum button head Dzus fasteners. They would be a lot easier to paint/annodize and won't stand out as much if left unpainted. I have used them on lexan side windows and places where the self ejecting type won't work:
Dzus Buttons