It seems to me that the basic point of randomizing the New World is not to simulate some sort of accurate geological model, but to simulate the lack of knowledge Europeans had, and thusly, the player.
Explorers don't know about plate tectonics. They don't know about weather patterns, desert zones etc... Adding real life rules to creating an 'accurate' model based on present day tectonic plates is just a crutch to give some players 'advance' knowledge of the New World. Knowledge the explorers just did not possess.
If you want to remove some inaccuracy, how about the one where the explorers don't have to return to the home country to show there discoveries? As it is, It doesn't matter if your conquistador/explorer is lost, you still get his discoveries.