Formatting a footnote to appear at the bottom of the page just represent too many difficulties for a reflowable format. It's hard enough to get right in fixed print.
The classic example is how to handle a 6-line footnote that is linked to an anchor 4 lines from the bottom of the page. You could just shift all 4 lines to the next page, but that would leave an ugly gap. Or you could put 3 lines of the footnote on the first page and slip the other 3 in at the bottom of the next (which removes much of the advantage of footnotes compared to endnotes and needs some form of marker). Or you could alter the page length on enough of the preceding and following pages so that the anchor point is shifted to a position where you can fit the entire footnote on the same page.
A popup box for footnotes is by far the most elegant solution, and superior to classical methods - those who don't want to read footnotes (which should, really, only contain superfluous information) don't even need to see them.
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