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Yes, there are differences between vanilla epubs and the socalled "kepubs" which are Kobo's own format. But if one is so inclined, one can use a plugin for Calibre in order to access most of the kepub-only features with regular epubs, such as the "pages per chapter" pagination and floating footnotes. Previously one could also access reading data (like, time remaining in book/chapter and a bar diagram of the chapter lengths) from within the book, but that has since removed, so now that is only possible with proper kepubs. It is unclear whether that feature will make it back.
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