All the fonts are baked into the PDF, so it should be readable anywhere; if it isn't, please submit a bug report!
But if you're looking for a format that lets you reflow the text, by changing the margins or font or text size, you're out of luck. The only way to write something like that is to bake it in from the beginning. That's easy for pure text, but hard to impossible for technical documents with lots of displayed equations, big hard-formatted boxes of text (ie, algorithms), and the like.
(Boaz Barak managed it by writing his Modern Complexity Theory book entirely in Markdown. The mind boggles.)
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.
I beleive that O'Reilly Media has used ASCIIDoc[0] as their preferred internal format for quite a few years. Formulas are supported through ASCIIMthML[1].
More recently, they seem to have transitioned to HTMLBook[2] as a preferred source format for systems like Atlas[3].
[0] ASCIIDoc is basically a Markdown-like (or ReStructuredText-like) format that is feature-equivalent to DocBook XML: http://asciidoc.org/
[1] http://asciidoc.org/asciimathml.html
The quality of the EPUB is terrible, it looks like it was OCR'd from images of the pages, not just converted from PDF.
Can you make the source format for the book available?