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The current output format is defined in Preferences->Behavior.
And why should mobi and epub be special? Why not EPUB and PDF? Or HTMLZ and DOCX? Or X and Y?
In any case, if you are using calibre to send your books to a device, there is no need to autoconvert at all. calibre will autoconvert the files to the format supported by the device when you click the send to device button.
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