Derek,
Sounds like 1/2 MDF + 1/4 or 1/16 lexan should be ok without routing. Install it as is and see how it goes. If you don't like the height, route out maybe 1/16 at a time till you find the height that you like. Don't take too much out or you will weaken the MDF too much. It's mostly about personal preference so don't be afraid to experiment.