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In the spec:
z-index is unsupported
position: absolute is discouraged
:hover may not be applicable (e.g. for devices with a touch screen)
and then there's issues with support and bugs in actual reading systems.
Footnotes are usually done as endnotes. Have an XHTML file dedicated to the notes, with pagebreaks between them, then link to and from them and you have a pretty workable system.
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