I have had a lot of powdercoating done over the years, and am currnetly in the process of powdercoating the cab of my hemtt restoration project.
Powdercoating is basically taking a polyester plastic colored powder and using electrical forces to cause it to temporarily "stick" to a part and then moving it into an oven and baking it at approx 300-400 degrees F. for 15-30 minutes. heat and time vary, but that is the general range. The powder melts down and forms a shell over the part you are powdercoating. Because heat is what melts the powder, heat is what will also burn it off.
I would strongly recommend that you consider using Jet-Hot Coating
http://www.jet-hot.com/ They will sandblast the inside and outside of your exhaust parts, and then coat them with a very high-tech ceramic material that is made specifically to hold up to high exhaust temps, and looks great for a very long time.
There are other companies out there that offer the same thing, but Jet-Hot has been around longest, and has a proven history of truly exceptional customer service and great work. I had them coat a motorcycle header I accidentally damamged a couple years ago, and they really impressed me with their work, and service. It really wasn't that expensive.
If you go ahead and powdercoat your exhaust, it will burn off in short-order.
I'm going to have Jet-Hot do my entire exhaust system from the turbo housing, manifolds, muffler, and all the clamps, pipes, etc. Should have it on in a couple months.