Three years ago, we machine-screw-and-bolt mounted both our joysticks under a plexi panel, a sexy ice blue (for our bot, Blizzard). I busted a gut trying to get spare joysticks (just in case) from CH, while waiting for First to give a definitive answer to whether this would be legal.
We got through GLR and the Mickey Mouse finals
with no objections, and no definitive answer.
My opinion is you can drill a few careful holes in the case, but don't mess with the internal circuits. (These joysticks are REALLY good, IMHO, but might not like the caress of a careless set of fingers messing inside.
In other years, we've used joysticks for steering, and separate "pots" not mounted in the joystick but in separate boxes for controlling other analog inputs to out machines. We didn't ever have to modify the internals of a joystick.