Here's a completely anecdotal, "a friend of a friend.." story, but I think it's a cool yi and you'll enjoy it: A friend of a friend is a cartographer who works in DC. According to this person, the official subway map of DC distorts the true geography of the city -- and the subway lines -- as much for security purposes as it does graphic design purposes. The red line, in particular, apparently is drawn with a complete…
But it wouldn't surprise me if an overlay on a cartographic map was intentionally inaccurate. One time I was in DC a cab driver was trying to get me to my hotel. His GPS went totally nonfunctional when we were in view of the Pentagon.
It would be an interesting research project to ride around subway systems with a data-logging accelerometer (like a smartphone). Integrate acceleration to get velocity, integrate velocity to get relative position, get GPS fixes when the signal is available, and diagram the results.