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.

The book has exercises that you can type out, execute and debug in the pages itself.

Agreed. I'm interested in this book, but the format is unbearable!

Just search for the pdf version on Google.