Supposedly, the backstory was that Vader and Ben had a duel and Vader fell into a volcano, and then it became a lava planet or whatever in ROTS. But falling into a volcano doesn't necessarily = no eyebrows, lol. I'm sure some burn victims re-grow hair in areas where the hair follicles weren't totally destroyed.
I'm totally willing to suspend disbelief enough to accept that the back of his head was more injured than his face. I mean, the skin on his face didn't really look like a burn victim's either & he has lips, right?! Don't most people with severe facial burns loose their lips? Maybe in the next EXTRA-extra-special-edition they should digitally remove his lips!
;-)