The guys over at
https://github.com/janeczku/calibre-web/ have been working on something that does allow one to hijack the Sync feature and point it to a Calibre-served library instead.
I've never tried it myself, I don't know how far it's gotten since I last looked into it, it might not have hit a stable release yet, and it might require some tinkering, but it was damn cool nonetheless.
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And there's of course @sherman's
UNCaGED which allows connecting a Kobo as a Wireless Smart Device (and which will see a new, more user-friendly release Soon (TM)

).