Also, I haven't written any books, but I wonder if Markdown is the best choice for a canonical format. The syntax is lightweight but also limited. For example, it doesn't support tables, and doesn't differentiate between source code (which should be syntax highlighted) and literal text (which shouldn't). You could define your own extensions, of course, but that breaks the compatibility feature. I think reStructuredText (for example) might be a better choice, although Emacs' Org-mode is my personal favorite document format. I suppose that in the end, whichever's most comfortable for the author to write in is the best.
edit: I should mention that this is in reference to a technical book because I've been thinking about technical writing lately. It just occurred to me that you could be writing the type of book that doesn't need tables or source code, in which case Markdown is probably perfect.