Dan Boney is awesome. I really like that he is sharing his classes and materials online (I would highly recommend his classes in Stanford[0] and his coursera class[2] as well).
I think this is still a work in progress / draft so don't expect to have an ebook available yet.
But it's 400 pages and part II and III are not present :|
Also I find the structure kind of odd. I is symmetric, II asymmetric and III protocols. Where do you put lattices, ZKP, lattices, FHE...
Another thing that bugged me: in the Integrity chapter they talk about MAC. Whereas they should talk about hashes, MAC provide integrity + authentication.
This is a common misconception that integrity is enough to protect against a MITM, whereas no you also need authentication. I'm sure this could lead to people just using a hash to secure their data in transit.
For those who are interested in number theory and its computational aspects, Victor Shoup (co-author of Dan Boneh for this book) also has another awesome book - http://www.shoup.net/ntb/.
I have two answers, the best one and the immediate one. The best course is to reach out to the authors and see if they will publish the LaTeX that it was used to produce that PDF (or, of course, see if LaTeX is epub aware or such).
The immediate answer to your question is that I only just now tried pdf2htmlEX (https://coolwanglu.github.io/pdf2htmlEX/) and was stunned how good it was. If you are on OSX, one can "brew install pdf2htmlex" your way to happiness. Don't get me wrong: exporting to HTML is a long way from "ebook-friendly" but I feel it is close to the spirit of your question.
Please report back if they authors do agree, as I'm sure you're not the only one interested.
[1] CS*55 series [2] https://www.coursera.org/course/crypto2