I think people are missing the distinction between modeled geography and modeled political situation in this discussion.
The Chernarus geo model is based of a real location in the Czech Republic. You can look at it in Google Earth.
The sea in the game is basically a river in real life in the south and east. It's fun to fly through the real villages representing the game villages. I lost my KML file, so I can't link that, but look at this video.
I'm sure Takistan is also based on some real geo data location.
The geography model clearly does not come from the political area they are modeling. It's pretty clear that Chernarus is based on the post Soviet areas, quite possibly Chechnya. But I also think that they haven't attempted to base it on a specific and actual location or situation, but distill the fundamental factors in a conflict area. This allows for more freedom to change the situation and create different campaigns and missions. Otherwise, everyone would constantly look for connections, find errors, controversies, and they'd be pigeon holed into a historical model.
Also clearly Takistan is a distilled middle east conflict, most closely Afghanistan, but Zargabad could easily be Baghdad.
Not naming it a real place is not because they are hiding the fact, but it's obvious that it's not actually intended to be a specific real location, but a generalized version that people can identify with, but not be put into somekind of historical simulator and the hassles and limitation that would come with that.