You can't fully top mount without having exposed bolt heads.
You also can't top mount it, and then put graphics over it, without routing deeper for the joystick, and then routing a coverplate for the joysticks, or entire CP, anyway.
If you bottom mount them, you will need to fill over the T-nuts with something, but don't really have to rout them.
You can just counter sink them slightly with a forstner bit, so that they sit just slightly below the level of the CP.
Put temporary bolts into the T-nuts from the bottom, to keep the threads open, suck them down tight, and then putty the top, over them.
That will give you a smooth top to put the graphics on, but not let the hardware show.
You can still run your dustwashers on top, if you want to.
Oscar has good pictures
HERE of how everything will come together nicely with a true Williams bottom mount.
That's basically exactly how I did my Crazy Climber CP, except that I glued an extra piece of 1/4" wood over the top, rather than messing around routing a piece of plexi in to cover everything.