I've not yet encountered the popup window for footnotes. But it seems to me that for the popup to be good it should render the whole text of the footnote in a scroll-able popup window superimposed over the book page window. They really wouldn't need a link to return to where you were reading if they did it right. They would only need to allow the popup to close when you touched the screen outside of the popup box boundary. This method would mean you never left the book page or position on the page. But we are talking about Amazon here, so I suspect they will do their best to muck it up!