I have never seen painted on dots, although I supposed it's possible. The dots I have gotten on Pitbull necks (as well as on other aftermarket necks) are made of plastic and are a fairly cheap in lay.
This is my experience as well. I've only done one PBG kit with a maple neck, but I'm quite confident saying the fret markers are not painted on. Also, IME maple fretboards shouldn't require any significant sanding (if any at all) unless there is some defect that needs fixing.