Just add the books from the Kobo library to calibre. Don't send them to the device. When calibre sees the device, it will match most of the books on the device to the books in the library. That will give you the best of both worlds: epubs for use elsewhere, and kepubs from Kobo with the in-book stats and syncing if you have other devices.
You can also use the book the Kobo desktop application downloads. But, you need the Obok plugin that is part of the DRM tools to add these to the library. That will give you books with the kepub internals, but the books are added as epub. Again, the book should get matched to the books on the device when you connect it.
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