You make some good points. Digital technology absolutely makes it easier to design books. No doubt about that. The problem with digital publishing is that (at the moment) you have limited control (even with pdf) over how the reader will see your 'book'.
The format of a book, the font, binding and paper should ideally complement the content—that's pretty hard to do if you read all your books on one e-reader. Now, don't get me wrong, nice books have always been a niche product and will remain so. I have no problem with that and many (maybe most) texts will be fine in electronic form. I just wanted to explain that there are some aspect of paper books that can't be replicated in e-readers.
It is masked but always present. I don't know who built to it. It came before the first kernel.