You are right that having two saves is somewhat confusing, I think I will look into doing away with the per editor save for the future. So when you perform any action on the book, the action automatically uses the latest text from all open editors, without needing to save first.
As for detecting if a link is to an element at the top of the file, that is certainly do-able, however, not particularly high priority. Feel free to ping me about it after Tweak Book is released.
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