The wording has some ambiguity, but it does sound like TFA hasn't heard of Xerox or Perq - perhaps attributing some misplaced invention, rather than popularisation, to Apple.
Subsequently reinforced my suspicion:
> The spirit of the Macintosh spread throughout all of computing; the GUI was inexorably the future.
I think with desktop minimalism there's two broad interpretations - a desktop metaphor that is simple (has (frustratingly) few features), versus one that is complex but can be configured to be simple to operate.
I like the fact I can very precisely adjust the width and colour of my window borders, but it's not a configuration item I visit more than once every few years, so I wouldn't say the option adds to the complexity of the interface. (Disclaimer - I've never used MATE.)
> Oddly enough, only GNOME has had any kind of distinct vision
The author did use KDE early on (version 3, but says they've only been using a computer for a decade and change).
They're aware of other desktops, then, including the one that's arguably put the most effort into having a consistent user experience.
The discussion on navigating through minimised windows I think boils down to a consideration of how to represent complexity - similarly their discussion of the launcher - almost inevitably a hierarchy is required if we are aiming to 'avoid the keyboard at all costs'. People have different GUI preferences there - mine is generally narrow and deep, over wide and shallow.