I actually don't really see any evidence in the article that the author believes any engineers would ever be happier in a smaller company. I'm not sure where you're seeing that softer view in the text. It's basically calling anyone who doesn't want to work for Google deluded.

It's not as if everyone in tech works for a startup, though I'm sure it often seems that way from the valley. Most likely the vast majority of engineers do in fact work for large companies, so the hysterical tone of the article only makes sense if you think even that small fraction of the industry that works at startups is fooling themselves about what makes them happy.

Of course, the article also seems to believe that most startup founders are engineers, and I'm not sure that's at all true either.

Then it's bad, misleading, imprecise writing to say invariably. A single counterexample does disprove it, by the definition of the word. If the writer didn't want the argument blown up like that, he should have looked among the other hundreds of thousands of words in English to find one that actually does say what he meant.