[lazyeye]

I find it easier to do this using kepubify in a script

https://pgaskin.net/kepubify/

[freeAgent]

I believe Calibre (very) recently added a feature to make conversion to kepub automatic when transferring to a Kobo, so things may have changed on the ease of use front.

[theshrike79]

It used to require a 3rd party plugin, but now KEPUB support is built in.