Of course, the agility here happens by accident, because in the first week of the program increment you realize that something is much harder than anticipated, and hundreds of person-hours of planning are thrown overboard.
I don't like SAFe for many reasons but I have seen it used successfully as an agile steppingstone. Some of the more original ideas with in SAFe (there aren't many) can even be useful. Anyway I don't think the idea of an ATO is a bad idea or anti agile. Even within an agile environment projects can exists and can be done in an agile way.
Due to badly run prince2/PMI projects people are allergic to anything remotely sounding like a project. So I get the autor when he thinks of ATO == PMO == PMI == waterfall == nightmare. But for larger organisation you will properly need something like a ATO to be successful. Like anything else a badly run, top down driven ATO will fail and make life difficult for anyone involved (this is also made clear in the original McKinsey article).
I like your balanced thinking, in writing the article I was trying to be balanced as well.
Unfortunately when I've seen ATOs in practice it's a band-aid to addressing the actual problems (usually leadership or leadership needing to make structural and large cultural changes).
Of course, the agility here happens by accident, because in the first week of the program increment you realize that something is much harder than anticipated, and hundreds of person-hours of planning are thrown overboard.