Never had anything powder coated before, but I've heard that it's good not to let the coating into any threads or threaded holes, as you will have a hard time threading anything on to the frame (bottom brackets, rear derailleur mounts, water bottle mounting bolts, fender and rack stays on rear dropouts,.....etc..) being that PC has quite a bit of thickness to it and is quite hard to take off....
So remind your powdercoating to block off those holes before they apply the finish. It could even be a problem with unthreaded holes on the frame where a close tolerance slip fit for components is required, like the brake caliper pivot bolt hole on the fork and seat stay bridge, so protect those from powdercoating too. Same with downtube shifter bosses, you can't have powdercoating on those and in their threaded shift lever mounting holes.