In practice it wasn't too uncommon for a single web page to also be a constellation different interdependent swf files. One for each menu, button, forms, etc.
The author's points hold true at least somewhat if you're talking about a single cohesive Flash application, but much less so if you're talking about a website built with flash.
Yes, flash websites were a bit of an anti-pattern even then (brilliant jewels like Homestarrunner.com aside)
Point I didn't mention clearly enough was that single-file-as-default was REALLY good for flash portal distribution. Made it easy for creators to share and easy for portals to ingest files, AND to "steal" them from eachother, which was something us developers actively encouraged, it's how you got your game or cartoon played/watched by millions of people.
The author's points hold true at least somewhat if you're talking about a single cohesive Flash application, but much less so if you're talking about a website built with flash.