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Unfortunately this is a bug with the kepub reader that happens even with books from the Kobo store when the <rt> tags are written for individual kanji instead of being unified per word.
In your modified edition, I think it should work even in kepub if you remove the <span>'s, since it's the way I see it's written in some store books I have in which the selection of words with furigana works correctly. In the majority of books it won't, though, because the <rt>'s are coded in per kanji.
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