I can't speak for all Connect books, but the one's I've purchased have the external ToC linking to an internal ToC inside the book with an external entry of Table of Contents. As for it being slow to change font sizes, it could be that because the reader has to do the work and the bible is so large, that it's just slow. But once you get the size you want, you need not worry about that. As for why footnotes as slow, I cannot guess.
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