If it's a nightmare for a particular team, that team just needs to learn how to use IB. One person (or one pair if you're doing that) should work on a scene at a time. And it's really easy to have storyboards broken up into multiple storyboards, which makes most of these red herring issues go away anyway.
I think people get fooled by the fact that the UI is visual. There it is, in front of you, so you think you should be able to add multiple interdependent constraints while another person with their own copy of the same file is adding conflicting interdependent constraints to the same scene. Note, I didn't say "independent" I said "interdependent." That will never work, ever, in any system. It won't even work if you do things programmatically, with different people changing interdependent constraints at the same time and then expecting them all to merge and work without pain. It's not even really an IB issue; you just see it in IB because the visual UI makes you think it should just work like magic.