http://www.icombinator.net/#_home is a reasonably decent example, its very obvious from reading the source that it is easier to read and understand (I am not even sure I can remember what vspace="" does). Instead of duplicating inline styles for every element you use minimal markup and use CSS to style the page. There are a few advantages to this: CSS caches, dynamically generated html with inline styles do not, its easier to edit, click inspect on the page and change some of the css, the whole page changes, you dont need a change + reload cycle.

Lots of people apply custom stylesheets because the default one has a lot of flaws, or sometimes they just want to. See http://userstyles.org/

The fact that this website works terribly on mobile is unarguable.

Web tooling means the browsers inspectors tools, the css overrides plugins, there are millions of plugins / enhancement tools and most of them can only work given a reasonable set of html and css to work with.