Whenever I installed a kit into a cabinet with a metal control panel, I'd tape a piece of cardboard over any holes that needed to be filled, then apply bondo in the hole on the underside.
Once dried, removed the cardboard and sanded down the bondo until it was flush with the cp. The the cp overlay goes over the metal, and lexan sheet over that.
On more than one occasion I'd get a game from another store where a kit was installed and they didn't fill the unused holes up. So of course customers punched through the cp overlay eventually.
I know some of the repairs I did wouldn't really stand up to what you're looking at for a collector.