Those aren't what this article is talking about though, For a huge client facing desktop web app, you can load things up front, expect the user to wait a bit, and then off you go.
But imagine if every page on HN took ~15 seconds to load. Heck the reddit mobile experience right now is that the comments section takes 4-5 seconds to load, and sometimes it doesn't load at all. Of course it is instant in their mobile app, and also instantaneous in their legacy mobile view. (Which makes me seriously question what in the world the modern mobile site is doing.)
Most content is temporary and short lived. Caching a script does next to no good if I only ever visit a site once or twice a month, I'd prefer there not be a script at all!
In regards to content, HN is one of the most valuable sites I use. The JavaScript is so tiny as to be inconsequential.
Give me a CNN.com that is as responsive.
Need to resize the browser window to get a good column width, but that site is fast.
(pure black on pure white also isn't easy on the eyes, but plain ol HTML can change that as well! :) )
Edit: the article mentions CNN, which is a mostly "static" site, but has enough JS to take 13 seconds to load on the "average" phone.
The only way to achieve something similar on the Web is to stick with canvas and WebGL.