Don't do footnotes with <aside>Don't do footnotes with link to an anchor. Have 1:1 relationship, so if a footnote is referenced 3x then repeat it 3 times. Have an anchor where you put the footnote link and link the footnote back to it.
Works on EVERY epub2 platform and also on ALL Kindles if the same epub2 is uploaded to Amazon KDP. Might not look as pretty, but works.
For very short footnotes and paragraphs not too big, then right justify the note* inline just after the paragraph.
[*This is a short note, marginalia style]
It's a mistake to try to have unreliable features (pop-up footnotes) or too closely duplicate traditional paper layout.
I know technical and academic stuff can need them, but they are not just a pain to create, but also to read. Breaks the flow even if a pop-up.