No, they would have earned a lower overall return, net of fees. That's the point of the rebuttal article, the original NYTimes piece was a hatchet job.
The article is based entirely on an assumption 10x higher than Vanguard's institutional fees. He declares it cheap relative to mutual funds, which is an absurd comparison.
The lower bound of his fee comparison is 8 basis points, which is 4x higher.
Not to mention the condescension dripping from every word. This piece is a good example of how not to write an 'informative' rebuttal.