The game is not changed at all. The FPGA on the cart is sniffing for the button combination. The is no game data altered at all.
it's also not unreasonable to think that children and or some unruly button-mashers would accidentally push the shortcuts.
My reason for wanting to disable them is exactly that. my DDR cab has a PC with a J-Pac and people accidentally push the shortcuts all the time... how they manage to to step on the correct arrows while holding both start buttons is beyond me, but they do it.