I built a control panel using 3/4 inch MDF and 3/8 inch Lexan. All the controls worked fine, and I didn't have to modify anything. I've got limited experience with arcade control panels, so maybe if I'd routed the bottom of the CP the joysticks would stick further up or something and I'd like it more -- but I can't really tell right now. I did have to cut out a hole in order to use the Oscar Controls joystick mounting plate, but otherwise I didn't have to route anything out.
In retrospect, I probably should have used 1/8 inch Lexan, I think. 3/8 was way too hard to work with. If you've never used Lexan before, you should read some about working with it before you start. Let me know if you want some (hard-learned) tips.