I actually doubt that "flush left only" and "no hyphenation" are the only, or even standard, options for most readers. But I think there's a synthesis possible

I actually doubt that "flush left only" and "no hyphenation" are the only, or even standard, options for most readers. But I think there's a synthesis possible between what you mean and what OP meant: ePub readers are somewhat better at adjusting to the reader. "Reader" here in terms of both the device and the actual human. Text can reflow, columns are used only where they make sense, and settings can be changed. PDFs are better at allowing the creator to, well, create. I know there's a hard core demographic that doesn't believe in any sort visual design. Yet there are topics and authors where choices of placement, font, color etc. are made with intent, and to good effect. Everything Tufte comes to mind. It should be possible, with something like Apple's Book Author, to create such designs that work well within the e-Book format. But I haven't seen any examples, probably because I rarely read textbooks these days and tend to buy paper copies of such books, anyway. In as far as I have seen illustrations in non-PDF formats, the results are dismal, with all sorts of sizing problems etc.