I think the reason why the rockstar developers chose this route for the train because in snail trail the train is passing by your main train its coming from Los Santos To San Fierro and because you only unlocked LS and SF in snail trail Las Ventures has been unlocked yet so that's why the train goes for the invisble route from LS to SF and the back to LS again.
The basic explanation that I heard long time ago was the train route was prepared then the map terrain change for some reason while the rails collision was left behind with the changes of the map. Since the train and othe vehicle is supposed to be disappeared after it's exist the certain are from the character, they did not bothered to change that. But they forget that the game is full explorable open world so we find their funny mistake unintentionally.
