Structurally, the most challenging book I've ever read was "The Message of THE QUR ĀN" by Muhammad Asad.

Start with the fact that the QUR ĀN itself is extremely non-linear. So much so that I think that this alone requires a great deal of study to address.

The text is 2 columns, the original Arabic adjacent to his English translation. There are copious and often long footnotes. The footnotes cross reference other footnotes, sometimes in chains. I read only the English.

I had to read it 4 times. Once just ignoring footnotes. Again, this time including just first-level footnotes. Again, following footnote chains back to their sources in the text. Finally, to reread just the text after pretending that I had everything figured out.

It took me a year to get through it to my satisfaction, although it was not the only reading, or even major project.

No way, that's on my to read list for completely unrelated reasons already

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.

1. If an appendix looks like "prerequisite" material, I read it first.

2. 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.

Tolkien had a very unique medical condition; absolutely massive appendix

Gotta mention House of Leaves, too. Another double bookmark book.

It's my experience that they're depicted as somewhat awkward hyperlinks in the book to the (howeverthefuck thevpublisher formatted them) footnotes and back.

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.

That's nothing compared to reading Ulysess, already a giant tome, and carrying the even bigger annotations as a separate book around with it, that you need to look at roughly every other sentence.