For popup foonotes, you will need to use kepub. The RMSDK renderer used for epub will not do popup footnotes.
You might also want to try adding either text-rendering: optimizeLegibility; or text-rendering: geometricPrecision; to the body class in your stylesheet for kepubs.
Personally, I don't like these since when I tried them years back, they did odd things to the spacing between words especially with justified text.
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