1. absolutely we should have a single-file, portable ebook format, and since PDF doesn't reflow text then it's not that.
2. HTML + CSS in 2024 is capable of reproducing virtually any kind of printed medium, but it can also reflow text.
3. I don't personally think JS should be a requirement, but a lot of conversations break down at this point so let do my best to explain and please understand I'm not simply being religious about this. In my view, an ebook is a book that can change its size in a way that makes sense. Bearing this in mind, I believe that if a reader has JS turned off, this book should work as intended. In other words JS shouldn't be required for it to perform its basic function. However, if there is some necessity to add interactivity or to augment the book, then yeah, why not, use JS. That's what it's there for. However, from the perspective of being a book, if it doesn't work as a book without JS then it's a bug in my view. (for standard ereader capabilities, I think the browser should offer that, but the book itself shouldn't be shipped with an ereader)
4. I think it's a mistake to embed all the styling as that may violate some people's CSP's. It's safer to specify separate styling as resources relative to the HTML, and ebooks should forbid loading resources from a separate domain. In this way, ebooks would always work offline, but it has the added benefit of working online too and would automatically adhere to the strictest possible CSP. This achieves the same goal as offline, but in a safer and more universally compliant way.
5. Finally, just distribute it in a zip file. That's how ebooks already work right?