Isn't the reason why Fixies often have powder coating on the rims is that they don't use brakes at all, hence no wear?
If you're going to do it and use brakes then the best idea would be to mask off the braking areas or have then remachined afterwards. I would have thought that brake blocks really won't work on powder-coated rims, or at least aren't designed to unless of course the fixie fashion has spawned a cottage industry making PC specific brake blocks.
Oh and don't have the whole wheels powdercaoted complete, break them down and only PC the rims otherwise it'll look like a stolen bike from the local estate that someone has sprayed