Actually most people I know who do a full paint restore to their cars including the wheels do the body first and then the wheels. What they do is have the car painted and then when that's done they take the car and the wheels to where they're getting the wheels recoated and let that place match the powder paint to the car. It's easier to try to match a smaller object like a wheel to the body paint then it is to try to match the body paint to the wheel. But what I suggest you do is call the places that do the powder coating by you and see which they prefer to do since some places like to do it the other way around.
As for using regular paint on the wheels as opposed to powder coating them, the regular paint won't be as tough or stick as well to the wheels as the powder coating would be and you'd take a very big chance of the wheels getting scratched and the paint either coming off, chipping or getting gouged off if you ever by mistake curb your wheels if you use regular paint since the paint is more or less just sitting on the surface of the wheel. With the powder coating on the other hand, all of those things are decreased since the pwder coating actually bonds with the metal of the wheel and more or less becomes part of the metal, rather then just sitting on the surface.
But good luck with whichever way you end up going.

And you're more then welcome for the information.