Painting stainless steel with anything eliminates the "stainless" part of it, and you can get rust in airtight pockets under the coating. What prevents rust on stainless steel is a layer of chromium oxide, and if you prevent oxygen from getting to the chromium (with a clearcoat, etc) the steel can rust just like normal steel.
That said, it may still work fine, just don't be shocked if the stainless does funny things under the clearcoat.