When I first got into ebooks I tried buying everything in them. It really sucks when you have a reference book at home, but you need it at work. Unfortunately, code formatting is often terrible for ebooks--reflow ruins it. So I tend to prefer the PDF or a hard copy for anything that contains code.

For narrative books I prefer EPUB all the way. Release both if possible!

It also sounds like a lot of books a proofed as a PDF (I hear a surprising amount of publishing is still driven by MS Word). Like the article says, the author may not have a version of the book with proper layout.