The identical file is pretty theoretical, yes. But if it tries to deduce origins of parts of files which were modified before commit, then it becomes more plausible. I noticed that you said that it "rarely" happens, rather than using a stronger term. :-)
Will you at least be able to see what guess git made before you commit? Although I'm not sure what you're supposed to do if you see that git guess wrong if you say that the only way to override the guess is to rewrite git...