Another problematic aspect is if one has poor eyesight and wishes to use a larger font size. One ends up having to scroll horizontally for each line of text for single column pages. For two-column pages, one has to scroll back a page after reading the first column.
Sometimes one can use a landscape-oriented display to avoid horizontal scrolling, but even if the same word count fits on the screen I seem to be annoyed by the low line count.
Providing large type and huge type PDFs would not entirely solve this problem as sometimes even one with poor eyesight might prefer a smaller font for scanning/skimming. Having to acquire two PDFs and switch between them based on mode of use seems suboptimal.
Fixed paged presentation has significant advantages for familiar reference material; some people seem to have a spatial memory that makes finding specific content by flipping pages faster than trying several search phrases (with the occasional benefit of serendipity).
Poetry often benefits from not reflowing lines and page breaking within a stanza is often more jarring than within a paragraph of prose. Yet a reader might prefer inferior typography over having to use a magnifying glass or carry a very large display.
One might be able to get some of the advantages of paged media for figures and tables by having header (or footer) pop-up links to such content when it is on the same "page" as the displayed text. This is not as low effort as moving one's eyes, but it might be better than inlined presentation on a small (relative to font size) display.
Even with print, there would be times when breaking the text to fit a figure is more disruptive than having the figure on a separate page. There would also be times when all the relevant figures would not fit on the same page as the related text.
Having a separate booklet of illustrations might make going back and forth between text and illustration easier, similar to having a lexicon or commentary open while reading. However, that also introduces position tracking in another book and other inconveniences.
Even when my vision was better, reading academic papers distributed as PDFs (usually 2-column) on a computer screen was less enjoyable than reading similar material in a reflowable format. Academic papers also do not seem to benefit as much from pagination as other writings.