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Creating an epub file and a Mobipocket file is quite different from a publisher point of view.
For the epub version, they can embed and use fonts like on a real book, add some extra formatting and support a lot more metadata.
That's the main reason why it's much better if publishers did create their e-books using epub, and then Amazon converted these files to Mobipocket. Part of the information is lost during this process, but at least these books are ready for epub or any other format.
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