Isn't "the purposes of the two formats are basically orthogonal" actually the entire point the article is making? Literally the first line of the summary:
> Research spanning 20 years proves PDFs are problematic for online reading. Yet they’re still prevalent and users continue to get lost in them.
From the second paragraph:
> The [PDF] format is intended and optimized for print. It’s inherently inaccessible, unpleasant to read, and cumbersome to navigate online.
The bolded statement in the second paragraph that's clearly meant to be the One Important Thing to Take Away:
> Do not use PDFs to present digital content that could and should otherwise be a web page.
Your comment here is eloquent, but the article's argument is not "print-layout documents should be replaced by hypertext," it's "print-layout documents are a poor fit for reading on screen-layout devices." When you conclude:
> It's all a matter of opinion over whether you prefer print-format documents or hypertext, and that's going to be very application-specific.
Aren't you essentially restating the article's thesis?
I don't want to read an article online that's a PDF for largely the same reason that I don't want to print the web version of the same article rather than a PDF. It's generally going to be clunky. The print page size and dimensions are not going to be my screen/window size and dimensions. I certainly don't want to read two- or three-column text on screen, which may require zooming in and out and scrolling back and forth on the same "print" page. And God help me if I'm trying to do that on my phone or iPad mini.
The article isn't saying "PDF is terrible and nobody should ever use it"; it's saying "PDFs were meant for specific applications and in nearly all circumstances, online reading is not it."