I've pretty much given up on Kobo's footnotes. If I could even get the same behavior with the same footnote structures, that might be acceptable. But, I really don't know what to expect from any given footnote. I've opened a Issue on that very github site jackie_w linked to:
https://github.com/kobolabs/epub-spec/issues/59
I've written them emails to their support page. I've even commented in some of the bug/wishlist threads here just in case anyone from Kobo ever popped by. No responses from them. That github page doesn't look like it's even been visited by anyone Kobo-related in 7 months (to update the readme). The last time an Issue was closed was over 2 years ago.