Calibre uses the drivers to communicate with the devices. Hence, file naming on the device is up to the driver. The built-in KoboTouch driver handles the renaming when sending a kepub from the library. The KoboTouchExtended driver inherits this and hence does exactly the same thing. The renaming of epubs that have been transformed to kepubs by the extended driver is handled separately.
In any case, it is working here with either driver. I can't think of a way it could fail. To take a guess, run calibre in debug mode, send a kepub and post the log. Hopefully it will show there.
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