It does seem a shame to paint over the aluminum spinner but I think I'd personally match the chosen paint scheme. Of course you'll have to touch up nicks and paint chips over time, but you'd have to keep the bare aluminum clean and occasionally have to buff our scratches too, so it's probably equal work keeping it nice either way.
So I think I'd paint it, myself. That said, last mustang I built, I bought a colored spinner that was color-matched to the monokote brand covering I was using. It was also red nose and tail but not really matching any historical scheme except for a generic tuskeegee red tail sort of theme.