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At this point, the KoboTouchExtended driver only works when sending to a Kobo ereader. You could use the Kepub Output plugin but that will store the kepubs in the calibre library.
The few times I've wanted to do a save to disk and convert to kepub, I used calibre to save to disk and then ran kepubify on the output folder to generate the kepub.epub files. I used a batch file with "kepubify --inplace --update path/to/directory. The --update meant I could recycle the directory without reconverting and the --inplace keeps kepubify from adding -converted to the file name.
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