I've done this on 3 Clear Coated playfields.

1st..buy new drill bits. Regular wood are fine, but make them sharp! Old bits have a risk of chipping.

2nd, just drill out all the way (wood rails). Presumably, the hole will be very slightly smaller due to clear coat. Just use a drill bit whose diameter fits the hole tightly. Your running it just to get some of the clear out of the diameter. With the bit being sharp, it should not chip the clear coat.

3rd, Install the rails.

Separate from the rails, I clean up every drill hole on the playfield.