I have been thinking about this program for a long time now, and one area I haven’t seen covered are references that work even across different versions of the same document (e.g. the book got a new version, but still has the same chapter more or less unchanged, or you highlighted something based on the epub, and switched to the PDF). Hypothesis’s implementation works quite well, as they were sort of forced to handle it due to web pages always changing (they store some of the surrounding context).