The most interesting clue in this mystery is that it seems especially bad when you open the same storyboard on a Retina display as opposed to a non-retina display.
At first I was going back and forth between a 4k iMac and a pre-retina Macbook pro and was getting a large volume of changes (~300 lines altered each time).
Then I simply dragged the xcode window from my main monitor (4k/retina) over to my second monitor (2560×1440, non-retina) – and while the window was the same size, xcode resized all the elements and complained of ~50 misplaced views. I moved it back to the retina display and about half of the “misplaced” errors went away, but half remained. The re-scaling – as you suggest – degrades the underlying data.
If you’ve got multiple developers working on the same file, this is bound to happen frequently.
The solution? This is likely all on Apple to correct – I haven’t run into any settings that would mitigate it otherwise.