Yes, the hotrod does have some wood cut out to make the joy the right height as I have one. On my newer control panels, though, I didn't bother doing countersinking the joys in the 3/4 MDF. Yes, the joystics are shorter, but IMO I don't think it makes too much of a differene anyway. I loved arcade games back in the day, but I don't remember them THAT well as to recall how tall the joystick was. So making them perfectly "arcade authentic" was near impossible for me anyway. Even if you don't "countersink" your joystick, you'll still be able to play whatever you want. However, You may want to make your joystick hole slightly larger than your button hole so the joystick isn't restricted by the wood.
wee beastie