Somewhat embarrassingly, 2.0.1 is released. Improvements here are not crashing when sending non-ePub files, and an easy choice between ePub and KePub uploads.
The consequence of that latter change is that the 'Extended Features' option only enables/disables the Kobo spans and JavaScript addition; all other options are now executed regardless of the 'Extended Features' option.
The consequence of the former change is that the plugin does what it's supposed to and I get to go bury myself in a book and try to forget I missed something so trivial