I'm extremely novice any any of the train code effects/physics, but from my memory from years ago, the train would purposely pass through everything/anyone 'but' the player it was launched at.
This allowed it to spawn mid-building, and not injure 'innocent' players.
No idea how that was done. I imagine if you tied physics to it, you'd have to make it intelligent to noclip through everything except for the player, and maybe world underneath it.