This is all nice and well, until your footnotes are half a page of explanation that was impossible to fit in the text directly.
At that point, I think pulling it out to an appendix is the right thing to do. Whenever I find a book with appendices, I do one of two things.
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If an appendix looks like “prerequisite” material, I read it first.
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If it looks like “further reading” or “deeper dive” material, I note where it’s referenced in the main text and return to it later.
The main reason I prefer footnotes to end notes is the separation of concerns. When a book has end notes, they are usually mixed with citations. I don’t mind managing 2 bookmarks or the eReader linking back and forth, but I really dislike following the reference to find that it just points at a whole other book.
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Reminds me of reading the print version of Infinite Jest by David Foster Wallace, where you needed one bookmark for the novel and another for the endnotes, which made up like 20% of the book. Hopefully e-readers make that easier now.
Depends on the reader I suppose. But in my expirances, its much much worse. You see, in a book you can quickly flip back and forth between pages. Moving bookmarks takes no effort. On a ereader you have to pick your page via a menu, go go your book marks via different menu. Delete bookmark via menu
Menu menu menu click click click its awful.
Got a book with a map at the front? Well you better memorize it because its not worth the effort to flip back and forth when ever some location comes up.
On the phone I think I would use two e-reader apps and just switch them. :-D