The unpopulated fan header is intended for a main board cooling fan that will start if the board temperature goes above 55C.
The first version of the boards that had the additional fan header will not work without a small hardware modification (the first version were sent out between August and September but no dates were actually given).
Per support team the fix requires “reversing the small mosfet (SOT-23) upside down to make it correct”. I ASSUME the one adjacent to the fan header. The “design engineer made a mistake that reversed the package”.
The newest versions being shipped should have this correction already applied. A firmware update may also be required. Motion Controller Ver 26 should support the fan header for the board cooling fan.