Shimano uses their PCD numbers to describe the circle that runs through the center of the spoke holes. This is the number that most written references about wheelbuilding call the flange diameter, and is the number that the classical spoke length formula (which most spoke calculation tools use) is built to take as its input. So the basic answer is use the PCD and ignore the other one.
The other number is the outside diameter of the flange. There is never a time this is pertinent to a hand or small production wheelbuilder. It's there so that producers with automated lines can know which hub loading machines are compatible with a given hub before making their orders. For example, whether you can use the little Holland Mechanics hub filling station, or if it needs the big one.