That sounds good; AFIK the fan controller works by switching the fan ground pin on the connector to gnd, or leaving it open, controlled by a N-channel mosfet in the normal Arduino manner. In theory you can use this to drive a fan off any reasonable (0-24v) psu so long as that psu's OV (gnd) is common with the Duet.
Similar to that other discussion, I'm doing exactly this on my cartesian's RAMPS board to control a 9v light rig powered off the 12v bus through a buck converter. Although the board is different, the principle and controller side circuitry is the same.