I think he has a good point, although it's not a clear analysis. I think it's important to realize that these games are made by the western entertainment industry and thus have many limitations. They aren't made by historians or social scientists. It would be interesting to note, however, how the Civilization series has been evolving from a binary Cold War perspective to a more multiculturalist view of the world. Just compare the victory conditions in Civ 2: space race and conquest to the newer ones: diplomacy and culture.
Simulations are abstractions of reality, they can never encompass all of it. And the scope of Civ can only exist within the historical conditions of the developers.
One classic example of this is the game Sword of the Samurai (1989), in which Sid Meier took part. You play as a samurai dynasty and your goal is to climb the social ladder and go from lowly samurai to emperor of Japan. This goal of social ascension says nothing about the Sengoku period, but it says a lot about the American Dream.