Also, MOBI does not support a lot of stuff with regard to layout that AZW3 does.
If you convert from AZW3 or EPUB to MOBI, you'll certainly lose a lot of markup. However, EPUB does support some stuff that can convert *really* badly to AZW3 (or maybe it converts fine, but the Kindle botches it up when displaying) for some reason, and then losing the markup by converting to MOBI is actually preferable.
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