But we could go so much further than reader mode. Users should have way more control over how content is rendered. But I'm something of an extremist. I don't really consider CSS/JS part of the web.
The stuff you're talking about isn't about browsers its about the websites.
If you had a website that uses javascript to parse MD or any other markup, spit it out as trivial HTML with light DOM, client-side formatting can do everything you want.
The problem is that modern websites use patterns that workaround users' capability to customize the presentation of the website. They do not want you to look at their site the way you want.
I guess the best solution to that isn't browser-side .md rendering, though.