> figures, footnotes and titles need to be presented in a deterministic way so that when text refers to a figure, or a footnote is referenced, etc, they exist in a predictable and know relationship to each other

Solved with references to the structure, e.g. ‘Figure 1.1‘ or ‘Section 2.4.‘

> If the text refers to a figure that is supposed to be on the same page, the author wants to be absolutely sure it appears on that page.

Why? Place the figure right after the text, or before it. “Supposed to be on the same page” is an example of thinking in terms of layout inherited from printed media. Delivering information doesn't depend on there being a concept of pages.

> have you never been to a web page where some images were not shown or just appeared as placeholder boxes?

Solved with a format that ships the page and images together, like Epub does. It's a basic requirement for sane personal storage-for-reference anyway.

> Device and image library and support limitations might lead to an image not appearing at all

Image support is solved with standardization of the format, as are many other formatting support features. If one wants to read docs on something less capable, like low-end devices, they take a conscious trade-off for the risk of something being unsupported.

> or at an unpredictable relative size so it's not easily readable

Don't quite see what kind of issues you mean here. Size relatively to the text is rather easily specified, and afaik normally honored unless the image is of some wild proportions like extra-wide.

But actually, I really wish that browsers and readers could zoom in/out on any image. I already do this frequently with Mac's ‘zoom’ tool. It's probably not even too hard to implement, I should look into finding or making a browser extension for this.

> such as with bad gamma or transparency settings, or with colours not shown with fidelity. This can actually change the meaning or interpretation of a result.

Interesting point, however I'm hard-pressed to see practical instances of this. When academic PDFs are explicitly made to be printed, apparently usually on office or home printers, I doubt that high quality of the result is to be expected. In this situation, authors should probably opt for rugged but dependable looks in most cases, with simple gray-color graphics and easily distinguished shapes, since even color print is not of much certainty. If precise color graphics are necessary then the paper is not fully readable in the printed form favored by many people, and I guess they will have to refer to the images on their computer—though even then I doubt many of them calibrate their monitors. So, I don't see much difference with HTML being read on a phone or a tablet an ebook reader, especially since phones and tablets have pretty good screens and support for HTML features. Finally, for strict reference, precise graphics can be delivered as attachments in a stricter format—just like it's done nowadays for large color visualizations, afaik.

> Information that belongs together, that the author intends and needs to be together, had better be together.

Again, put images after text that pertains to them.

> These formats can't guarantee what fonts information will be represented in

Why is that necessary? For math symbols, Unicode has several variations like Fraktur.

> they can't even guarantee whether text will he shown in italics, bold

Sure they can.

> what relative font sizes they will have

Subtext and supertext are respectively smaller and larger than the normal type. What else is needed? Do people write “let polar coordinates be denoted with type of 36 points”?