Well, Org is suitable for small notes. But for the scope of this book, it's difficult to make Org work for such a complex layout (largely because I don't want to mess with the CSS).
I used Lyx because it enabled me to focus on the content without all the markup text. Writing Latex in Emacs can reduce the distraction, but not enough. I just wanted to focus on the content at the time. Learning Latex is difficult enough, learning how to use the major mode at the same time doubles the difficulty.
Obviously, I still use Emacs daily for writing code and other things. Just not for writing book.
