To check the bolts the maximum of the load required for the operating case (WM1) or the seating case (WM2) is used.

Now, to check the flange the code adds abuse factor to account for the fact that "bubba" in the field could over tighten the bolts and cause overstress in the flange. Moreover, if the flange has leakage it is common to re-tighten the bolts.

This is how it’s done,

Am - required bolt area

= Max( WM1 / Sb, WM2 / Sba )

Ab – available bolt area

W – flange design bolt load in gasket seating condition
= Sba * ( Am + Ab ) / 2

Hence, the flange is designed for average of the Minimum required bolt load and total bolt load (before the bolt fails).

This what the program does.