As above, it ensures a good level of finish and adhesion. I am currently getting my RA's refurbed and they are being shot blasted and then chemically stripped to ensure all the old paint and any corrosion are removed before the new powder coating goes on.
Obviously it costs more than just getting the face of the wheel touched up/painted, but you do get a much more complete refurbishment, ie the entire alloy, not just the face, and the level of finish is on a par, if not better than, when the alloys were new rather than trying to simply paint over up any problems. (Also I read somewhere that it was bad to paint alloys?! but I don't know that reasoning behind this statement.)
If you are going to spend the money on getting a job done, you might as well do it right I say...