This sounds like a fascinating book! It's always interested me how book covers are made, why they pick the scene or elements they do, etc. It seems you'd get the best results if you knew what the book was about.
Apparently it's a hotly contested issue, at least that's what I gathered from the designer's comments. Some of them take notes or mark scenes; some of them try to get a general gestalt. A lot of the nonfiction designers, though, say they only read a bit of the book, or sometimes just the blurb provided by the publisher. I kind of think it showed, though...