Actually, the 747s that serve as Air Force One and its backup incorporate features and parts from both the 747-200 and -400. The engines and systems of the two planes are 747-400 components, while the body and wings are 747-200. The planes also incorporate military technology, including missle countermeasures, special radar and in-flight re-fueling systems. There's alot more to it than that, but I'm just going by what I remember from what I've read on here.
Anyway, it's pretty obvious as well that if the US government goes to Boeing and says, "We want two specially-made 747-200s" and gives Boeing all the specs, that is exactly what Boeing built.