Clear coat is hard. That's why we like on our play fields.
A minor difference between the surface of the play field and the inserts is so minor that ball travel is not going to be affected during game play. A dirty play field will have crap making a home on the surface of the play field that would do more to affect ball travel than the minor surface difference between the play field and an insert. The clear is hard enough that you will not need to worry about flameouts around the inserts.
Once you have the play field populated and installed, plastics on, the play field glass on and play field lights on, you are not going to notice any minor imperfections visually in the surface.
Now, if you are are going to enter a pinball contest, and the judges are going to remove your play field glass and ding you for any minor surface differences they can feel with their fingers, maybe you would want to go to the extreme.
But if it is going into your line up for playing action, I say build it up, install it, wax it, and play on.
Clean it with Novus. No problem, but a coat of wax will not harm your clear coat and IMO my pins play better after a fresh coat of wax. They play faster, the ball will get all squirrelly with extra spins and English moves---which is action I like.