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After creating a valid EPUB 2 or EPUB 3 file, I am often able to run the file through Amazon's kindlegen convertor, and assuming neither file was overly complicated in terms of page layout, have the resulting mobi file look pretty decent in the kindle viewer.
That being said, does kindlegen do better with converting EPUB 2 specifications or EPUB 3 specifications to its proprietary format?
KindleGen will work equally well on epub 3.0 and epub 2.0. Just make sure that you're being consistent throughout with the structure—you can't use an epub 3.0 toc.xhtml for navigation in an epub 2.0 document, for example. As long as you have a valid epub document of one flavor or another (validated with the current version of epubcheck), your file should be fine.
A special note for fixed layout files: Early epub fixed layout was an iBooks-specific format. Much of that format was adopted by the IDPF into the epub format, but it's not completely integrated. If you have a fixed layout epub that you want to run through KindleGen, make sure that it's epub 3.0 fixed layout, or you may have errors crop up.
Well kindlegen basically just strips all code that isn't on Amazon documentation from HTML and CSS. So if your ePub is not too complicated the results should be satisfactory. This can change when you will try convert fixed layout where hierarchy of DOM isn't logic.
To give you straight answer: It not make any difference unless your DOM is in logic order.
DOM (Document Object Model) define structure of an document. Ideally structure (or hierarchy ) should be logic in terms of rendering. For example:
<div>
<p>Lorem ipsum</p>
</div>
<div>
<p>Lorem ipsum 2</p>
</div>
here you have two divs with two paragraphs one after the other. If you will not manipulate with them, they will also render one after the other. But you could use CSS or JS to manipulate them and render <p>Lorem ipsum 2</p> before <p>Lorem ipsum</p> without change your actual HTML. This situation happens very often when you designing fixed-layout ePub which are parto of ePub3 spec.