Ah. OK. Now I understand what you mean :-) There are reason why I don't provide more generic sample to test on other readers:
- We don't support other readers officially.
- KCC by design can't create generic files. All images are processed for specific resolution.
But if you choose "Other" profile and provide screen resolution of Kobo - you will get what I consider clean EPUB 3.0 output. Which is really not clean as it will have slightly bloated CSS/HTML due some hacks and styles used only by Kindle. And AFAIK that file render correctly on e-ink devices other than Kobo and Kindle.
Also entire matter is hindered by fact that I don't have access to any Kobo hardware. My work in this case is based on user feedback.
EDIT:
Kobo for PC also display file list as TOC completely ignoring NAV and NCX.