I agree, the flange calculation appx.2 is lacking specific information, like every bolt requires a hole and don't drill more holes than needed for the number of bolts used in calculations. It is indeed confusing. Is not prohibiting either the drilling of holes radially, in the edge of the flange. In fact, is allowing the drilling and tapping of holes for lifting eyes for large flanges. It does, however, specify in the clause 2-3 (definitions), that A is the OD of flange or the diameter corresponding to the bottom of the slots extending to the edge of the flange. That means the material extending along the slot to the edge of the flange does not count for strenght. It is similar to the sizing of the clamped flanges, you can make slots until you run out of material.
However, the length of the ligament between bolt holes is related to the thickness of the flange, that's the reason one cannot keep drilling holes in a flange calculated for a number and size of bolts/bolt holes.
cheers,
gr2vessels