Yes, I painted over the amber marker/turn signal. Although, I left the bulb in there so my blinkers wouldn't hyperflash.
I have zero loss of light now that I painted the inside of the lights. This leaves the projector unobstructed and I get full brightness with my Morimoto HID kit on stock projectors. However when I had the Lamin-X film tints on, this did affect my headlights but I was still able to see well thanks to my HIDs.