An example of why layout matters, and not just textual matter, Derrida's
Glas:
http://en.wikipedia.org/wiki/Glas_(book)
Here, he writes in two columns (one a commentary on Hegel, and another on Genet) with interweaving quotes. I'm not sure that in other digital book formats aside from PDF would work for this kind of text.
I too have composed text where the layout is part and parcel of the way one engages with the document. A long time ago I wrote a "mystoriography" interweaving a second set of voices between lines of the main text.