- I can imagine authors feeling frustrated if someone reaches out about a problem in the HTML version of their paper, but they have no way to correct it except by hoping that a change to the PDF fixes a change to the generated HTML. Easier to just fix the formatting problem in the PDF outright.
- It would be neat to allow people to experiment with alternative formatting for their papers. For example, imagine a paper about a programming language that embeds a sandbox you can use to play around with the language under discussion. Or a paper about multivariable calculus and you can interact with a three dimensional plot of some function.