Yeah, kinda.  Basically.  I mean, it's the kind of thing where, for example, having compared the distances between the aligned locations of *all* the reads from two different BAMs, we now want to ask the question, "how many reads were aligned to different locations between the two bams?" and the answer is, "the number of reads whose pairwise 'positions' metric was non-zero."  Or, in the case of duplicate flagging, "how many reads were marked as a duplicate in one ADAM file but not in the other?"

And these methods are here to allow us to ask and answer that question generically.  But I think it deserves a little more thought and work, so thanks for flagging it!