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.
While browsers like Chrome and Firefox normally render very well on-screen any Web page, it is enough to give them the "Print" command for that page, to see in most cases a badly rendered page, where the size ratios of various elements are bad and they overlap or are mis-positioned so that the "printed" page is completely unlike what the browser shows on screen.
The way how the "printed" pages look in Firefox and Chrome demonstrates the same rendering problems that appear in most EPUB readers.
I have no idea which is the cause of this, but the bad behavior of "printing" in Firefox and Chrome has existed for years. Not all browsers behave the same, e.g. Vivaldi usually is much better at generating "printed" pages, than Chrome, despite being derived from the same code base.
Perhaps the great differences between on-screen rendering and "printed" rendering is caused by the fact that badly designed HTML/CSS might specify some sizes in "pixels" or other such inappropriate units, instead of using length units, like points, inches or millimeters. Then when rendering on different media the size ratios are corrupted.