PDF compare tool does not play nicely with footnotes
When comparing two pdfs, identical text will be marked as changes if footnotes have changed location (by changed I just mean bumped to the bottom of a different page due to increased or decreased length, even though the marker is the same place in the text).
This is a function of the fact that Adobe sees footnotes as part of the text and so thinks the ordering of the text has changed.
This is related to the issue where Adobe does not maintain footnote status of smaller text at the bottom of a page (often under a line) when exporting from PDF to Word.
Kelly shared this idea