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In x-unified and x-compare modes, it should never be possible for there to be two data with the same x-coordinate and only one of them is displayed in a hoverlabel. I know compare mode doesn't currently behave this way but I consider it a bug.
The solution proposed by @alexcjohnson seems good to me:
Step 1: find hover points the way we do now
Step 2: loop back over traces not in the set of hover points we already found, and see if any of them have a point with position-axis value exactly matching what we found for the other point(s)