It depends on the body shop. Many body shops do not have full wheel refurb facilities and instead rub down and respray, because it is quite a complex and specific job in itself. Whereas a wheel specialist will dip the wheel in acid to remove the old paint and lacquer usually for 24 hours. Then they will fill, weld, heat treat or rub down the area to bring it flush with the alloy, then they are bead blasted to create the best surface, then put through an oven to remove all trapped air before priming. Then they will be primed, put into another oven, then either powder coated or sprayed and lacquered.
A specialist wheel service will be the same price as a body shop but the process is much more specialised and QC is higher as its the only output product.
I see what your saying but depends how anal you are, had mine done at the wheel specialist and had them done again because I wasn't happy with how they had finished them. With a careful eye you can definitely tell the difference, you can usually feel the difference too with overspray. Then there is the problem with lacquer overlap, the wheel is much more likely to corrode when rubbed down painted over lacquer instead of being done properly, which happened to my old car, the previous owner had a cheap smart repair done and the paint came off due to corrosion because the paint doesn't adhere to the surface in the same way so it might be cheaper but in the long run you'll have to have it done again.
