PDF serves an important purpose; it’s not an abomination. It conveys exactly what the author or publisher intended. HTML can not do this. It can serve as a reliable archive and be made (imperfectly) accessible, as described in the article. Of course all this comes with significant tradeoffs, including reduced interoperability, as you say. But there are good reasons for academic publishing, especially in math, CS, and physics (but also in some areas of the humanities) to prefer PDFs—it’s not just obstinacy.