Manufacturers will put that on their helmets so they aren't held responsible if someone chooses to paint it. There is a chance that painting a helmet could weaken it but as long as you don't go throught the gelcoat into the carbon or glass fibre and ensure all the eps is masked then there shouldn't be a problem. I use water based automotive paints that cannot harm the eps or shell as it's the solvents in solvent based paints that can melt the eps. Also stickers that are solvent based could do the same as that's also why you're told that stIckers shouldn't be applied. I would also never paint a damaged helmet and prefer to paint new. Troy Lee seems to have done well out of painting helmets.
Anyone interested in a custom helmet let me know.