I've noticed at or near last light that the yellow shows up much better than the red or green. I imagine each pin has a different color to make confusion less possible. Assuming I can keep which pin is which straight, does anyone have any reason why I shouldn't make them all yellow or at least the ones set for yardages I'm most likely to shoot from in low light conditions?

Make yellow your 20 yard pin, your not going to shoot are far distance in low light so the others don't matter.