This particular BoB (and I have three of them), uses the 12-24V supply to drive the 10V regulator (LM317) for the 0-10V spindle control, as well as the opto-isolator inputs.

The 5V supply (either via terminals or USB) is used for the logic devices (and therefore the drives to the stepper controllers).

To the OP - if you need to use the E-Stop/limit inputs, as Clive-S says you'll need that 12-24V supply - or that'll be your next problem.