the train man would need to be in the matrix to be taken over by smith. the train station is between the real world and the matrix. seeing as how the train man is the only program who can go in and out of the train station via the train, i don't see how smith can manage to go into the station without the aid of the train man, meaning the train man bargained for his existence or smith just copied over him and used his knowledge of the train and the train station... unless smith has a wi-fi connection like neo...
we really dont know if he took over the train man. or merovingian, for some reason i think he copied merovingian but he could have hid in the train station.
either way smith ruled the matrix world and if he couldnt do a thing in the train station it doesnt matter. in time he would have. eventually he would have overriden everything. it was a matter of time.
Like the defected program (virus) Smith became, he was meant to spread throughout all the system.
The only reason Smith looked human was because that how the Matrix was designed, or at least that's how the team plugged into the matrix interpreted the information.
Thinkin' about it...I'm not sure if Smith copied Merovingian and his rogues...or even the Architect himself.
When Smith copied the Oracle, he was granted her powers of precognition...and he became as powerful as Neo. If Smith copied Merv, Architect, etc.....I don't see how Neo could've even put up a fight during the last battle.
I don't think Smith did copy everyone in the entire Matrix, I mean we're talking about the entire planet, that's over 6 billion people to copy in the short amount of time that was meant to have passed during the 2 movies, Matrix Reloaded/Revolutions, I'd estimate he converted everyone in the city, also I don't think he did convert the Merovingian or his men, it would have been awesome to see Smith trying to fight his way to the Merovingian, however the Merovingian could have either used a back-door and kept running, or gone and hidden in the Train Station under the protection of the Train Man along with his goons. Also just to clarify, the Train Station isn't a part of the Matrix, it's a link between the 2 worlds. Also the Architect's office isn't a part of the Matrix either, it's like a control center that watches over the Matrix, without that key and the building security down, it's impossible to reach, so no I don't think Smith converted the Architect either.