Evan,
I took voluminous notes when reading Musicphilia, which has footnotes for every other paragraph (not an exaggeration).

I’d click on the footnote link and then press the ‘Back’ button to get back to my reading. But when I quit reading, it always knew my last reading page — so at least on SOME books, they seem to check whether a nether-region in the back belongs to a set of footnotes.

The footnote pages were so interesting I sometimes read a bunch of them at a time but it didn’t mix up my actual last-page for body of the book.

(It may for other books.)

It could also be that I always pressed the Back button to get back to reading.