Now that the shaft and coupling have been "fitted", including the set screw spotting, the flange is mounted to the shaft and placed in the lathe.
When using a split coupling it is very, very important to properly and evenly torque the clamping screws. Not doing this evenly and properly can result in the face being out of round with the shaft. When facing the shaft coupling the machinist will properly torque the clamping nuts so you get a perfect facing with no run out.