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I've never felt the need to patch. I've looked at kepub, but it's unique to Kobo and the only advantage is zooming images. I hardly ever reading anything with footnotes and there are different ways of doing them so they don't always do the kepub popup box.
The regular epub on anything that observes CSS seems better than Kindle.
So down to personal preference. You can turn kepub on the fly on/off from Calibre epub on the Kobo driver, or switch to the one that doesn't do it.
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