Book is epub 3, and the Kobo supports epub 3, and renders some of the footnotes as popups as indicated. And it works in most other books, except those where there's a very large set of foot/end notes to render all at one time. So I think epub version is not the issue here, everything is 3, every apps works (except Kobo, which only works part of the time).

This *may* be by-design behavior as you suggest rather than a bug. However other apps are rendering the specific note, including KOReader, Calibre's built-in reader, FBReader, Moon+, and even Amazon Kindle does similar for their KFX book. So I'd expect it's programmatically do-able, and at least there's some perception that some users would want that behavior. IMHO, it would make sense to enable this behavior to be configurable in device configuration or in user settings. I submitted a detailed bug/feature request to Kobo, will see how they respond.