Ha! Success!
Instead of dealing with kepub extracted from the desktop app, I've gone to
https://www.kobo.com/jp/en/library, and for every book, I've downloaded acsm file. ADE processed those, and provided me with completely nice and working epubs. On top of that, I went to
https://books.rakuten.co.jp and purchased two books there, paying with an EU card. Everything worked, and the books I've purchased there were also visible under "My books" on kobo.com.
This is really great!
Now, there's still
this bug preventing those epubs to display correctly in ebook-viewer, but I'll just use some different viewer.