The big problem is catering to different input methods. A mouse has far greater accuracy than a touch display. You can put two links mere pixels apart on a desktop interface and that is fine because a mouse is more than accurate enough. The smallest interactive element a keyboard-and-mouse user can hit is probably about the size of a single period in a font. There are other issues with doing that, I'm trying to highlight the sort of accuracy you have with a mouse. A mobile user could never hit such a small target.
On PC, you can enter text and show the full content of the website at the same time. You can search in the page with a keypress. You can open multiple web pages at the same time. That is not possible on mobile.
As more and more countries have aging population I'd expect these kind of accessibility issues to be more prominent. Sometimes I feel like using modes (vim style) could help, with the user getting different tradeoffs when "reading" and "manipulating", if there was an easy enough way to switch between one mode and the other.
At the end of the day people want magazine layouts, newspaper splash styles, postcard type areas etc. I think even novel writers/editors have a "best viewed at" size and layout in mind that gives a perfect pace to their story.
Html/css gives the tool to switch layouts and potentially adjust to make the best of the area offered, but it will probably always be a compromise in the eyes of the more opiniated designers, and auto-reflowing content would be more of a necessary evil.
Even in our field we have traces of that with our recommended line length, method length, bracket styles etc.
You point out web vs mobile, but of course as you probably use "web" as a shortcut for "PC", web also applies to mobile. Then on a 27" screen you might have one window full screen or 20 windows overlapping and an actual 7" browser to display the site. And others will be on PC, but with a 13" touch screen. And others on a 10" phone but split in half.
Then some people will increase text size and your design will need to deal with it.
Before you realize it you have dozens of constraints and requirements to think about, start dropping some to satisfy others, and inevitably people will be pissed at the result.