> In general academics prefer PDF to HTML. In part, this is just because our tooling produces PDFs, so this is easiest.
The tooling producing PDF by default absolutely makes the preference for PDF justifiable. However, tooling is driven by usage - if more papers come with rendered HTML (e.g. through Pandoc if necessary), and people start preferring to consume HTML, then tooling support for HTML will improve.
> But also, we tend to prefer that the formatting be semi-canonical, so that "the bottom of page 7" or "three lines after Theorem 1.2" are meaningful things to say and ask questions about.
Couldn't you replace references like "the bottom of page 7" with others like "two sentences after theorem 1.2" that are layout-independent? This would also make it easier to rewrite parts of the paper without having to go back and fix all of your layout-dependent references when the layout shifts.
HTML has strong advantages for both paper and electronic reading, so I think it's worth making an effort to adopt.
When I print out a paper to take notes, the margins are usually too narrow for my note-taking, and I additionally have a preference for a narrow margin on one side and a wide margin on the other (on the same side, not alternating with page parity like a book), which virtually no paper has in its PDF representation. When I read a paper electronically, I want to eliminate pagination and read the entire thing as a single long page. Both of these things are significantly easier to do with HTML than LaTeX (and, in the case of the "eliminate pagination" case, I've never found a way to do it with LaTeX at all).
(also, in general, HTML is just far more flexible and accessible than PDF for most people to modify to suit their preferences - I think most on HN would agree with that)