I’ve tried this and get weird errors. I followed the instructions carefully (I think!), do you have to do anything special to get it to work?
Not really, I did have to install and setup kepubify and i always convert the epub files to kepub manually (from the Calibre-Web page) after I upload new books, so far I only had minor issues when removing books from Kobo and suffered a random reset of the reading hours stat.
I also use a Kobo with Calibre-web and it syncs fine. It’s been about a year so I can’t remember specifics. I remember modifying settings in my Kobo to point to my Calibre-web URL and in Calibre-web settings allow Kobo sync and then make a Kobo shelf. All the books in Kobo shelf are what it syncs too