I'd push that a step further and say the problem is about data that's been rendered into a different form for human readability. The plain serial text of a magazine article exists in principle and likely wasn't written with ideas like column splits and image-wrapping at the front of the author's mind. 2sk21 advocates shipping that serial form instead of something image-like. That's what's machine-hostile about PDF: it makes the least semantically significant parts easy for the machine to discern at the cost of obfuscating the really important ideas.

Though as a counterpoint, separating content from presentation is already a fairly common practice.