I have never clear coated a pinball playfield so take this info as you will... but by saying this i do work with lacquer a lot at work.
My thoughts would be to just use a drill bit maybe by hand...turning it not as a punch.. from the top side of the playfield... going from the underneath may cause the top to crack or lift causing more damage... you could always try a battery operated drill... these tend to stop when the trigger is released and you can get a slower speed too by gently pressing the trigger, electric drills tend only have fast speeds and spin for a while after you release the trigger so if you stuff up for some reason you might scratch the playfield is some way... anyway give it a shot on a back unseen hole... maybe use a drill bit half the size of the hole first then move up to the correct size... hope this info helps...