Interesting discussions to me at least, but yes it has meandered a bit.

Bringing it back to original subject, can we agree that here are the main takeaways for ordinary Kobo/Calibre users (folks who are not devs) trying to get the most out of their Kobo device?

1. To get full functionality out of your Kobo, it's helpful to convert the books on it to the .kepub format. Kepub is just a slightly optimized form of .epub.
2. Converting to .kepub gives you at least these features:
- Faster, more responsive page turns.
- Better image handling, including display, zooming, and panning.
- Footnote preview (footnote link pops up in the page you're on, rather than going to another page)
- Better epub 3 feature support
- Better, more responsive text selection for copying, bookmarking, and annotations.
- Fast page flip (press lower corner, pages flip fast till you stop)
- Reading statistics
3. To convert in Calibre, just install the KoboTouchExtended plugin (developed by @jgoguen), which is not installed by default. That's it, no need to do anything else. Sync your non-DRM'd books from Calibre to your device, and Calibre does the work.
4. If you want to convert your books to .kepub without using Calibre for some reason, there's a command line utility called kepubify (developed by @geek1011).

Thanks all.