I could be wrong on this, but I'm willing to bet the paint wont last very wring on such a high contact item. That's why the handles are not painted, but made of a plastic that was colored before molding. I understand your delima though....I'm in the same position. One thought is to by a comp stick of the desired color and then get someone with a lathe to cut the groove in the same spot as in the 360.
Another possibility is this. I seem to recall that the wico leaf joystick handles will fit a 360. Maybe you can get one of these off of ebay or something and then remove the top and put a comp or ultimate top of the right color in its place. Again, I haven't tried this, I'm just throwing out alternatives for you.