The calibre driver will only manage books that are in the current calibre library. But, as kepubs can't be in the library, they can't directly be handled. But, if there is a book in the library with exactly the same title and author as the kepub, calibre will see them as the same book. Then it can do the shelf and series management.
When I buy a book from Kobo, I also download the epub version and add it to my calibre library. This gives me the correct details and the connection. It can also be done by adding an empty book in calibre. An empty book doesn't have any formats, but has the metadata.
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