Human memory is a funny thing. Overall, people are comparatively poor at remembering words and numbers. We’re much better at remembering various other things, so people set words to music because it makes remembering them
vastly easier. Spatial matters are like this too: we’re simply better at remembering spatial positions of things we’ve experienced than other linguistic references to them. If you ask me where the parable of the sheep and the goats is, I can tell you it’s at the bottom of the fourth column, and find it very rapidly, immediately framed in its context of all that Jesus was expounding in Matthew 24–25.
(That’s also why hard breaks at chapter boundaries is a horrible idea. They split stories artificially all the time. If you must do scrolling, make it infinite scrolling.)
When I have to use a different Bible from my primary one, it’s really hard finding everything I want to find, because it’s just not in the right place on the page! It’s similar for spatial memory of things relative to other books, or relative to the length of the Bible as a whole: you just get a better sense of how it all fits together. (That’s what I was going for with the parable reference last paragraph.) Accessing things only by references and searches and scrolling disembodies it and I am convinced does a great deal of harm in comprehension.
For purely reading the Bible, yes, PDF is a good solution. But that reduces it to a very poor imitation of paper, discarding almost all the potential strengths of the computer (weak search is the only one retained).
I can keep my finger in two or three places in the Bible and flip between them and other such things—it comes naturally and can genuinely be called intuitive. Unless you go skeuomorph, no interface for achieving anything similar on the computer is ever intuitive, and obtaining even halfway good ergonomics is extremely difficult. (A skeuomorph is no panacea here, but I think it can make things easier. My point is more about the conceptual advantages of the old medium, with a view to attempting to integrate its virtues rather than just discarding it because we’re on a different physical medium now.)