For what it may be worth, I took a look at the scrambled ePub. To put it gently, it's error filled.
Looking inside the file, the footnotes are at the end of each chapter and not in a separate footnotes file.
The KoboTouchExtended driver is not happy with it but a quick fixup seems to have helped with that and I do get popup footnotes.
Personally, if I received a ebook in such bad shape, I would be complaining bitterly to where ever I received it from.