I think this is a dramatic difference of opinion between coders and everyone else in science, if you excuse the generalization. I say that because of the large number of tools to try to one-up the PDF for academic scholarship (e.g. Readcube). Publishers looking to invent ways to define their own value have been slowly trying to force these things onto readers, but almost everyone in my field hates them and wishes they would die. Formatting and typography are critical in many fields, and a PDF is the canonical way to maintain these aspects of a paper.
