Good catch. I looked at the book I was testing with, and everything is in the root directory.
But, it looks like it might be simpler. From my testing, the only thing needed is that the text and OPF are not in the root directory. And it doesn't seem to matter what the subdirectory is called.
Also, Kobo do have some notes on the footnotes at
https://github.com/kobolabs/epub-spe...kobo-platforms. Reading those explains a few things, including why some ToC pages in books show the popup rather than act as a link.
I have attached the epub I have been experimenting with. The three chapters have the different foot/end notes I could think of. The back-links from the end notes all go the first chapter, but the "Previous location" in the bottom bar is probably the better way to navigate backwards.