If the book shows "KOBO EPUB" in the device's library listing it is a KePub. If it just shows "EPUB" then it is an ePub.
For sideloaded KePubs the KePub full-screen text cut-off problems can be fixed without a patch if you set up the KoboTouchExtended driver correctly, but I don't know about the KePub Output plugin.
There are two things that need to be done to the KePub to fix the problems:
1. A suitable wrapper div needs to be added to each html file. This is done automatically by the KoboTouchExtended driver, but I don't know if the KePub Output plugin does this.
2. The KePub stylesheet needs to be modified to add:
body { margin: 0 !important; padding: 0 !important; }
div#book-columns { padding: 0 0.2em !important; }
The KoboTouchExtended driver can be set up to add those to KePub stylesheets automatically, but it doesn't add them by default. I don't know if the KePub Output plugin can do this.
(The above applies to horizontal languages, use div#book-columns { padding 0.2em 0 !important; } for vertical languages such as Japanese.)
Edit: For details of how to set up the KoboTouchExtended driver to add the above CSS to KePubs automatically, see
https://github.com/jgoguen/calibre-k...-arbitrary-css