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There are a few differences between how Kobo handles books bought from their store and books that are sideloaded. Kobo has two different renderers: ACCESS for kepubs (Kobo's minor variant on epub format that they use for content bought from kobobooks.com) and Adobe for sideloaded. The differences are pretty minor: Adobe gives you the total pages in the book, for example, while ACCESS gives you pages per chapter. Minor stuff like that.
You can get a Kobo e-reader to treat all your sideloaded books as kepubs pretty easily. Calibre even has a plugin for it.
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