PDF is an attempt at non-Turing complete, simpler PostScript (PS). It comes from a time of paged media de facto ruling the world. Changing layouts was never the goal, because PDF was the output format.

In case of academic research papers typeset with LaTeX, the source file is something you'd likely want to consider the semantic equivalent of HTML. TeX should be able to render the same document with different output constraints ("responsive layout"), but because of the architecture (TeX itself is fully Turing complete), it is pretty slow at re-rendering an entire document.

Part of the allure of a static document format like PDF is that you can, in theory, fetch just page 454 of 6000 page document and render that: with HTML, just like with TeX, you'd have to get and render the entire document to be certain that the layout won't change after you've processed the whole file.