I have used a Kobo for the last few years, having switched from Kindle (though nothing wrong with Kindles in my experience), and have never had an issue with an Amazon purchase converted to epub or kepub (I favour kepubs because I happen to like the heading at the top and page in chapter count at the bottom, plus my Kobo is quicker handling a kepub).
I have also compared several kepubs directly loaded from Kobo to the reader against the same books sideloaded from Calibre and noticed no difference (other than that my Calibre "polished" version is smaller in file size) .
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