let me explain further. when you create the e-book, if you segment the book into small-enough sections, it'll generally work, across almost all situations, no matter how the person has configured the fontsize.
That's probably true enough for ebook readers (and I got good results for just epub using my CLI tools) but once I went to InDesign for the PDF layout using it for epub generation was no big deal and that was where I was making final changes to the text.
i'd be happy to show you how i'd do your book, if you'd be interested in seeing it, if you send me a copy of it.
Thank you. If you (or anyone else following this thread) wants to grab it I put up links at http://osc.justthebestparts.com/grab/
(If you need the actual markdown files I'd have to see about packing those up. I was writing the book as a Webby-generated site using a combination of Markdown and ERB. I had some scripts that would then use that same generated HTML to package it up as epub. )
It would be great if I could use command-line tools to generate the PDF while not sacrificing the precise look and layout I want but I'm deeply skeptical this can be done without a visual tool and manual adjustments to adjust things for aesthetic reasons. (Or without learning LateX. :))