@CyberPaul: Not without writing some code.
You can get calibre to convert the epubs to kepub by changing configuration of the Folder Device Interface. In the list of formats, move "kepub" to the top and deselect epub and any other format that you want converted to kepub. After that, when you send a book to the folder, if you do not already have a kepub version, it will convert the book to kepub and then do the send.
After that, you will still need to do the rename. The built-in KoboTouch and KoboTouchExtended driver have code to handle this because both know the books are going to a Kobo device. The Folder Device does not know this, and hence does not have anything to handle the extension change. And I'm not sure it should.
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