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There are some differences in the conversion to MOBI performed by calibre and Amazon's conversion of emailed EPUBs that are going to result in repeated questions being raised here on MobileRead as this feature becomes used more frequently.
On the plus side the conversion by Amazon using kindlegen results in both MOBI and KF8 formats being produced. So most Kindle users will see richer formatting and have access to custom fonts and the font boldness control which they would not have with just old MOBI.
Amazon's conversion also produces the tables needed to synchronize between MOBI and KF8, which are missing from calibre conversion. So if someone switches between reading on a Kindle and on an iPhone their reading position and annotations will sync properly between devices.
And there are some quirks in calibre's conversion that can lead to problems such as the indexer crashing on Kindles, which are less likely to occur with Amazon's conversion.
On the negative side, KF8 format personal documents on Kindle will only show a generic cover in the Kindle's library. That will bother those who desire proper covers there.
Also Amazon's conversion is less forgiving than calibre's when the source EPUB has problems.
One thing that is likely to come up often is how a lack of specification of the character encoding in HTML files is handled. This is often missing in older EPUBs and those from sketchy sources. In calibre UTF-8 encoding is assumed but for historical reasons Amazon's conversion assumes ISO-8859-1 (Latin-1). The result is usually seen as quotation marks turning into odd character sequences like ’.
Other problems, such as mis-ordered entries in the internal TOC, can cause the conversion to fail completely. In that case a generic error email is returned with no indication of what went wrong or how to fix it.
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