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Hairy Scot,
When you transfer a book from calibre's library to a reading device, there are certain things that occur. The metadata is updated (if it needs it) and various changes are made to the internal structure of the ebook. This can include a wide variety of things, including whether or not the book should have a cover image inside the ebook file. It also includes converting one ebook format to another.
Many of these options can be manually set in the Output settings. This allows users to optimize a book for their unique situation. So long as calibre's library has all the original data, you can create as many device specific ebooks as needed. (Keeping this data safe is why user's are told never to go into calibre's files and manually do stuff - you risk losing your data.)
Calibre does a fine job at automating things, but the process can never be completely automatic, although calibre comes close.
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