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I made a test with an EPUB2 file -- converting it to EPUB3 and adding epub:type="footnote" to the footnote <div> was enough for KOReader to render it in page. This might be easier to do than converting them to <aside>?
(I did get epubchecker errors after conversion where image width percentage values where used instead of integers after conversion, but the epub was working just fine; I used ePub3-itizer_v058 for Sigil.)
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