Part of the issue stems from the "strong data coupling" that's all the rage. Everything on the page should correlate at any given point in time. Add a character to a search box and the search results should be updated. The practical effect of this is that any single modification could (and often does) rewrite the contents of the entire page.
The other thing the article brings up is that developers and designers often disregard input flow. This may be partly driven by not having sufficiently dynamic tooling (Illustrator can hardly be used to design out flow patterns, for example.)
These two issues have a unifying quality: Websites must be "instagrammable", which is to say look good in single snapshots of time, and the dynamics take a serious back seat.