It will look so much better if you sand it flat, spray some filler primmer on and make it so smooth. Since you have to do it anyway, take the time.
However, i didn't use hi temp paint on my valve cover, it's holding up fine. I wouldn't worry. If it peels or bubbles, you are in the same situation. If you really like it, just throw it on and see what happens. I'm sure that sees less heat than a valve cover, it may work fine. I used regular rustolium. I'm about to do mine again, different color and plan to use the same as i found a color i love.