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I think the main problem is that: If you have a complicated, highly stylized ebook, there is just no easy way to maintain a single html source that will produce an epub and a mobi that are identical... regardless of the conversion software. This is not an issue with the conversion software, but rather, an issue of the vast differences between the epub and mobi formats. Those differences become more glaring the more complicated your layout becomes.
I'm not saying it's impossible, but there comes point, when it becomes easier (and less frustrating) to maintain two separate sources. That point is different for everyone.
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