I’d let someone else confirm, but I would sand them flat.

Yep, sand them.

I replaced every insert on my Surf Champ a few years ago and I can still remember the challenge it posed. I did not need or use a playfield overlay -- I was lucky -- my surface came up pristine after meticulous cleaning, polishing and waxing. I have done partial overlays of clear mylar over newly-installed inserts, and I can tell you it's not for beginners. Here's what you're up against:

1. generic plastic inserts ("will-fits") to replace the original, dried out, shrunken and cupped factory ones often have digits or letters embossed on their surfaces that need to be sanded flat. This is not a real problem. Yet.

2. I first dry-fitted every one to make sure it had enough material height for sanding. These are generics, and not all insert geometrics are exactly alike. A few were too loose, too thin or too wide (toss them), but most were too thick (too high.)

3. In my case, I progressively-sanded each top surface using low to high grit paper until I was satisfied with the finish. (I made a make-shift tool using wrench sockets and foam tape.) Then the thicker pieces -- more than half of them -- had to be sanded on the other (lower) side to be sure it would fit flush and snug. Again, I dry-fitted every one to be sure.

4. I then gave the top surfaces of all the inserts a few coats of poly spray and let them dry overnight. I used a sheet of cardboard with holes cut to stabilize the inserts and avoid getting poly on the sides. In the case of the ones with decals, I applied the decals first and let them dry, then sprayed them with poly. The final step was leveling and gluing each insert in place.

In your case of applying an overlay protector on top of the sanded inserts, you obviously won't need to spray them with poly. Your biggest challenge will be getting the heights of the insert and playfield surfaces EXACTLY FLUSH.

Good luck.