The point is that trains aren't halfway near as popular as they could and should be.
It's too basic a feature to force players to travel to the Boneyard or Vault City. It's not intuitive gameplay. I'd be fine with a quest that originated from the stations themselves, because that would make sense. That way, from the start, players would be aware that trains exist and that there is a way to get them running. You want to get trains, you go to the train station. You do the quest at the train station to get trains.
But having to look at the game's wiki page to discover that the quest, or even trains exist, is poor design. You can't expect players to go talk to every NPC in every town on the off chance they have a quest at this stage in the game, as there's just too few around.