Another aspect that often gets overlooked is the sense of place, letting the physical world remember relationships for you. Put your finger on an interesting passage, flip back to where you saw something related...about this many pages, left side, near the top,... there it is! Flip back and forth, comparing the two...ah, interesting, there's a shift of perspective.
You really can't do that with digital media, letting your proprioception carry its share of the load.
The same can be said of code. Editors fail to exploit the spatial reasoning and intuition we have. Imagine if source code were presented spatially.
The file paradigm w.r.t. source code could be included here as well, as the concept of file is incidental to the logical structure of programs. The logical structure could also be expressed spatially.
The problem is how? The only way I could imagine would be with something like apple vision pro and being able to place windows all around you. Sounds to me like more of a gimmick than a real useful feature.
I think we'd need to come up with something better than that. There is graphical programming like scratch and unreal blueprints etc, maybe that has some potential for taking advantage of spatial reasoning, but I still don't really see it being particularly revolutionary.
You really can't do that with digital media, letting your proprioception carry its share of the load.