@mike1889
I actually have a dedicated hotkey on the arcade controller. On the SNES pads I just use SELECT as hotkey. I haven’t had the time use the cabinet for some time now but at least I can’t remember having problems when swapping between the different configurations of buttons on the controllers..
In some cases using SELECT as a hotkey can interfere with the game controls but as far as I’m concerned the dedicated hotkey is not absolutely necessary. On the other hand I really wish I had put in two more action buttons on the arcade controllers. I now have Street Fighter style six button layouts but I wish they were eight buttons instead. They could be used as R1 and R2 on Playstation games. NeoGeo cabinets used to have four buttons in a row so having two rows of four buttons would mimic the NeoGeo controller better as I then could use one out of the two rows of buttons as originally intended. There’s probably also many other situations where more action buttons will allow for better configurations.
If you haven’t read this yet you really should, it’s a fantastic resource on arcade controllers:
http://slagcoin.com/joystick.html