My, now SBF's, drill is, to the best of my knowledge, the original colour. I got it from a dealer who'd got it from a school and I doubt either of them repainted it.
I’ve seen a lot worse. I’d be inclined to just leave it alone as you won’t improve the visual look of it by filling them up. As brad said you’ll just end up with a spotty table.
If it bothers you then as per PB said cover it with a thick plate.