[j2kun]

> I also don't understand why (academic) publishing is so PDF focused

Because academics still often publish physical books.

You prefer to have lots of tools and write custom extensions to programs. And you'll have to maintain those tools forever, and migrate them when the upstream software breaks, or the links you use die. Most academic authors don't want to do that, and with latex they can take the same typeset equations and diagrams (without learning any new tools):

  - Publish a paper
  - Write a talk
  - Publish a book
  - Manage a unified bibliography across all of these