I've done it many times including the Steve Vai handle on guitars and such.
If you have the right luthier do it you shouldn't have a problem. Dull bits and lack of experience will get you some chips in the finish at the edge of the route. . If that happens and the color is in the finish coat and not applied directly to the wood it may be real hard to repair.
You will also have to seal the raw wood inside the pickup route,especially around the edges to prevent any chipping after the fact. This work will be double the price of having the work done on an unfinished body.
Lower Groove Guitars - Tyranis 4
Lower Groove Guitars - Axiom 4
Lower Groove Guitars - Paragon 4
Demeter HBP-1J, Crown Power,
Eden D4X10 XLT (pair)
Radial Bassbone, DR High Beams,