I don't know what you use to typeset the book, as I can't find any source files, but isn't LaTeX really good at this?
I'm not sure what makes it hard to reflow. The text seems to be mostly paragraphs with figures, inline formulas and footnotes; pretty basic stuff, no?
(O'Reilly's books were famously typeset with Troff/Groff for many years, though I don't know how painful that was or how advanced their typesetting needs were.)
All I know is that I'd love a version that worked on smaller devices. I tried the Kindle version reformatted by archive.org, but it has lost most of the formatting, making it almost completely unreadable.
I'd especially like an HTML version of the book that was fully hyperlinked, with zoomable vector figures, footnotes hidden away in popups, etc.