This is a limitation of the device, not the format. Why do people expect to be able to read heavily formatted books on every device they own? For books made up mostly of natural language text, this might be a reasonable expectation, but technical books have a different set of design constraints that make them ill-suited to general e-readers.
This is a limitation of the device, not the format.
No it's not. The kindle works fine for programming books, I'm currently reading Bjarne's "The C++ Programing Language" on my kindle, on PDF actually. The book itself lies on my bookshelf but why would I bother to open it?
The PDF isn't tailored for the kindle but it has wide enough margins so that when you crop it it works quite well on the kindle. The kindle is not the limitation nor the problem.
The problem is rather the crippled format that you get in a fullsize PDF. What exactly are you going to read it on? Print it out? (seriously?). On your monitor? Not really... On your tablet? You're joking right, reading a book on a glossy LCD?
Having a book as a PDF is quite useless for other than using it as a reference.
Now I don't know about any potential issues with epub/mobi, and honestly I couldn't care less in this case. The site mentioned (and still does) that an ePub will be available and if so I kind of expected an ePub version of it, in my eyes that was an incentive to take the course.
If that isn't going to happen an ~A5 PDF will work great too, since there actually exist devices that you can read it on comfortably.
And I kind of have a hard time to see why the book, as it is portrayed in the HTML-version wouldn't be able to work as an epub - but OK, if that's the case (or if epub truly is just a mess) that's surely not the case for a portable-device-friendly-PDF.
Also, it really cracks me up to see someone talk about broken formats and in the same post make an argument for PDF.