I'm not sure if MX-S-SW24 denotes the default voltage setting or not, but the BAC-281 external controllers can all operate on 24V, 36V or 48V, so you will not burn out the controller.
If it's programmed for 24V and you run it on a 36V battery it should still work fine. Many users deliberately set the battery voltage setting to 24V when using 36V or 48V batteries because it seems to produce more torque.
Alan