I understand your point that you want a fixed presentation layout and pagination. I prefer to be able to responsively resize the document and to follow the ToC instead of pages. I've yet to see documentation that's thousands of pages long that doesn't include a very detailed ToC. For me remembering "section 8.3.16.2" is better and makes more sense than remembering "page 1292". I've had to read scanned math books years ago and I remember using some PDF reader to put bookmarks that correspond to the ToC, so I'd put "2.5.1.2 - Theorem about X" in the sidebar. That's how I was able to actually go back and forth easily. With just pages it would've taken me tens of seconds to locate a theorem (or lemma, proof, definition, whatever). And it was a dense book, so I had to constantly go back and reread stuff. But I agree that PDFs can, and often do, have ToCs, too.

> the size ratios between various elements may be inappropriate

I can't recall having this issue on websites or on EPUBs. What kinds of elements are we talking about? HTML and CSS are pretty good at keeping sizes from what I've seen. I agree that there are many EPUB readers, most of them very unpolished. And perhaps there aren't EPUB readers that are good at everything, yet.

For formulas, MathML and other tech has been satisfactory. I was able to find this basic math paper arXiv uses as a demo for their HTML papers:

https://ar5iv.labs.arxiv.org/html/1910.06709

It doesn't have figures, but the math is rendered perfectly. I can easily remove the "justify" style and increase and decrease the letters. If it was a long paper, it would've been nice to have a clickable ToC, but most EPUBs have one.

I think that right now most EPUB readers and some HTML renderings are bad, but I believe they'll get better.