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.