I had my frame powder coated. Paint in the east coast is getting more expensive because of the solvents. I found a guy that did work for DOD and he prepped it with a phosphor base and then powder coat. I guess the phosphor prevents rust in case of a scratch, a DOD prerequisite. The job was nicely done and it looked good when new. It looks like a 3 year old paint job now, it's not impervious to scratches. Prep is imperative, you must mask off the engine mounting points, I also masked off the trans mounting points, the swing arm and the z plates plus the fuel tank wings, so I could get good grounding throughout the bike. Ended up I didn't need any extra ground wires from the original harness. I have had some problem areas where I had to remove it for welding, but I just painted it with a brush and rustolium enamel and it matches pretty good, especially where you can't see it as an obvious thing. I'd do it again.
I also had the fork trees, the front mudguard, battery tray, trans mount, swing arm and I wish I had the oil tank done, but they suggested not because of the sand blasting.
It's up to you, but I suggest you go in after the frame is stripped and guide them through the masking process, it's really too much work to take it off. Oh, don't put it on where the rear axle mounts too, you'll add about 3/8-1/2" of extra space on both sides of the swing arm and the brake plate. The powder coater should have all sorts of masking materials and circles to place on the pertinent places. Forget the OB method of nuts/bolts/washers, there are plenty of stick on plastic masks the painter should have that are impervious to the heat.