We experimented with this back in the early days of Heighway (2012), but there were three real drawbacks. One, it was incredibly easy to break the screen. Two, being LCD the screen could only darken, not lighten, and was completely incompatible with any art below it no matter how much light there was in the game. Three, it created a kind of 'prism' effect which rendered the game unplayable to anyone with dodgy eyesight who wore glasses.
A transparent OLED screen might have worked better had they been at all cost effective, but ultimately the only real solution is to wait for a cheap enough screen you can cut through and shape, and use it like a playfield protector with all the mechanics and fixings placed through it, and on which all the playfield art, lamps, inserts and interactive effects can be displayed.