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Don't use PDF conversion as a basis for comparison. A PDF file is not a book, and doesn't contain text, hence is extremely difficult to convert.
ePub files generally convert pretty cleanly to Mobi. You may get the occasional quirk, such as a drop capital (which ePub supports, but Mobi doesn't) finishing up on a line by itself, but that's about the limit of it. Generally speaking, conversion from ePub to Mobi will work well.
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