These kinds of crackpot articles surface every couple of years in the mainstream press, always from people who demonstrate no knowledge of Chomsky's work beyond having read the back cover of his 1965 "Aspects of the Theory of Syntax."
I didn't read the original article, but as described in the Ars article, the thesis makes absolutely no sense whatsoever. The fact that we may have a hard time reconciling how languages can be diverse in their handling of subject/object/verb order doesn't disprove the concept of Universal Grammar. In fact, it's an argument for Universal Grammar that we can even have a coherent conversation about the way all languages handle subject/object/verb order - Universal Grammar is not about providing a set of rules describe all languages, it's about explaining what a possible rule is, and you have to approach that with logic rather than statistics.
The Ars article talks about "languages that have been evolving for a minimum of 4,000 years," as if those languages simply sprung into existence a little more than 4 millennia ago with no relation to anything else. This is the linguistic equivalent of creationism.
[Edit: expanded acronym "UG" to "Universal Grammar" for clarity]