[ink-sniffer]

It would be amazing if footnote text could "hide" between the lines where the linked reference number is displayed and then appear directly in that position when the link is tapped. I guess this is only possible with JavaScript, which EPUB3 supports, but it will take a while until E-readers fully support that feature and I am really in doubt if I as a reader would want all sorts of scripts to mess up my reading experience.

I think the decision of putting the footnotes at the end of each chapter or the book itself relies mainly on the type of book you create and how footnotes are used. For non-fiction books where the footnotes include much additional information about the subject I'd put them at the end of the chapter, to have the reader occasionally stumble upon them and pick something up they find interesting. If the footnotes only contain information about quoted publications or things of less importance for the reader, I'd bundle them at the end of the book. Luckily, InDesign let's you make those choices by yourself and exports the Footnotes properly. You can even jump back and forth between the reference link and the link in the footnote text, so you don't need any back button.
It's all not perfect, but I think I can live with that.