I still can't understand why, once they have a free version available in form of a html page, they don't give also a free pdf version far more readable and portable.
Hi, I'm a researcher using a (massive) fork of the Runestone platform. I'm pretty familiar with their technology and group. They use sphinx to generate html pages that then interact with their website through ajax. Their entire focus is on an interactive web experience for their book. Techniaclly, sphinx can export to PDF, but I doubt they've ever tried (I certainly haven't bothered in my fork), because the core functionality that we both trumpet is the interactivity.
That said: if you print individual pages with Chrome's Print to PDF feature, I think you'll be pleased with the result. The formatting tends to be very good (without extraneous markup and such, except for the interactive stuff - which was never going to go well.
I'm sure there are ways to script that printing - if not, then there aren't so many chapters that it would get excessive, I imagine. Personally, none of my students have ever requested an offline version of the book, but that might just as easily be because they never considered the utility of such a thing.
I wouldn't mind hearing your criticisms of the interface. I use a fork of this book largely for the UI (not intentionally, that's just how things worked out). I am not a GUI-person, I just use Bootstrap as defensively as possible. So far, I haven't had any complaints about the affordances, but then most students don't complain unless things have gone terribly wrong. If you have specific things you can point to, it'd be helpful for my own purposes.