I would like to add another reason why it is critical that MN handle page numbers correctly.
You may not be aware of this, but the standard practice of academic discussion of any book or article is that somebody in the class or working group says: “on page X, the author says…”, followed by a discussion of a specific passage/chart/etc. Very typically, the discussion moves through the book/article, using page numbers as the point of reference.
Since MN doesn’t handle PDF page numbers correctly, it is basically useless in these group discussions or any sort of group collaboration with non-MN users. The MN “Go to Page” (Cmd-P) function is useless, because the page numbers are wrong.
That is, the page numbers being used by the group are correct, and trying to participate using MN you are immediately lost and must always convert between the book or article’s true page numbers, and MN’s broken page numbers. Similarly, the MN page numbers in the TOC cannot be given to the group, and you must always zoom out and look at the entire PDF page, to get the correct number. In addition, there is apparently no way to change the scale of the PDF, so the MN window and its sub-panes must be resized and adjusted, simply to view the entire PDF page.
Please consider prioritizing a fix for this. It is a VERY serious and frustrating problem.