Well, now PCC-1 is not a Post Construction Code, it is simply the first document issued by the Post Construction Committee. Given that separate committees are responsible for the books - and further recognizing that the B31 Committee has a relatively specific scope and the PC Committee has a much broader scope - it is not surprising that differences may appear in PCC standards and other standards. In evaluating which is the "better" approach, one must consider the particular circumstance involved, but generally speaking (yes, there are exceptions) the PCC standards defer to the original codes of construction for design details where such conflicts can exist rather than provide their own details.
Further, there has long been ongoing discussion about shifting PCC-1 into some new construction oriented standard (B31 would be one obvious committee to deal with it, but Section VIII can also easily claim some scope with its flanged components), since PCC-1 is not limited to post-construction only and has clear applicability to new construction as well.
Bottom line: I'd say that assembling flanged bolted joints in accordance with PCC-1 will result in the highest probability of not having flanged joint leaks. Consider what the scope of the committees is - the PCC-1 folks are 100% focused on this topic. The B31 folks have many other issues to dilute their attention.