The statements made by the article are related to something called Universal Grammar, it is not related to syntax theory or Chomsky hierarchies:
http://en.wikipedia.org/wiki/Universal_grammar
According to the article, Chomsky probably didn't invent universal grammar, but he was certainly a strong proponent.
As to the second point, the article claims that languages have been evolving for a minimum of 4,000 years, not a maximum of four thousand years. This is a perfectly accurate statement about all known species of animals. All it really says is that we have records that lead us to know for certain that certain sets of languages had common roots as soon as 4,000 years ago, but we are not sure about their common roots before that.
This sort of argument is very common in genetics; I recall reading a book about how human men can all be traced to a common ancestor 90,000 years back. This does not imply that scientists believe humans sprang into being 90,000 years ago.