You'll need to keep manually adding the .epub extension if you distribute converted books. I'd actually recommend against distributing KePub format books anyway though, because the format is still not identical to the official Kobo format, but if you want to anyway go right ahead. I won't add the option to use '.kepub.epub' directly.
If you're sending the KePub books to your Kobo device, try the option in the driver plugin to copy converted books to a directory. I can't remember exactly how I implemented that, but what you get is the KePub version of the book copied to a directory of your choice when it's sent to your device. I don't think it works when sending KePub format books, only when converting during upload, but see if that works for you.
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