I asked the same question when I had my Honda RS250 and I was told that you need to take them to a specialist like Dymag. Apparently they strip the old wheel and use a special coating before painting over. This coating will prevent oxidation between the magnesium and the paint. I noticed some of this oxidation on my wheels (looks like bubbling of paint).

So in summary, the feeling I got was to avoid powdercoating for magnesium but at least go to a specialist for any repainting and ask about what they do to prep the wheels.