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They're one and the same, as far as newer devices go (in both cases you'll get the azw3 file).
The pros and cons of sending a file from Calibre vs e-mailing it: when you e-mail the book, you'll get the option to sync with your other Kindle apps and devices. That said, I personally use the direct Calibre sending, because I want custom page numbers and syncing is not a high priority for me.
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