It wouldn't hurt to have this function, but my intuition is that its use will be minimal. If you are already working with sorted arrays, you already have a flop cost on that order of magnitude, and the optimized merge saves you a factor two at the very most. Using numpy means you are sacrificing factors of two and beyond relative to pure C left right and center anyway, so if this kind of thing matters to you, you probably wont be working in numpy in the first place.
That said, I share your interest in overhauling arraysetops. I see many opportunities for expanding its functionality. There is a question that amounts to 'how do I do group-by in numpy' on stackoverflow almost every week. That would have my top priority, but also things like extending np.unique to things like graph edges, or other more complex input, is very often useful to me.
Ive written up a draft
a while ago which accomplishes all of the above and more. It reimplements functions like np.unique around a common Index object. This index object encapsulates the precomputation (sorting) required for efficient set-ops on different datatypes, and provides a common interface to obtain the kind of information you are talking about (which is used extensively internally in the implementation of group_by, for instance).
ie, this functionality allows you to write neat things like group_by(randint(0,9,(100,2))).median(rand(100))
But I have the feeling much more could be done in this direction, and I feel this draft could really use a bit of back and forth. If we are going to completely rewrite arraysetops, we might as well do it right.