There is so much
OFF advice out there
1) The plugin works with the Calibre device driver, so it knows about the Kobo (model) needs.
2) Kobo can use EPUB or KEPUB so no need to make the Library have KEPUB just to read on a Kobo. There are additional features that can be gaind.

Look at the plugins (all those for Kobo) Configurations and see what they offer if set. I have 2 different Kobo. I even set backup locations by Serial (model)
3) The extended edition CAN convert an EPUB on the fly, the copy book being sent (the Kepub is only on the device) >>> This is a great reason to NOT backdoor (use the OS) to side load. (you set this on the 'Extended' tab. see image.
It has been quite a while, so I do not remember all what I needed to do...
But the PI works as installed. Configuration just gets you MORE and is the place where you tell it what custom columns (or folders) to use for that MORE.