Considering how the tracks run directly into a tunnel under Ul'dah, I can actually see it being used in a simillar fashion to the small ferries in Gridania and Limsa Lominsa - allowing quick transport to and from the city to Black Brush or near the zone to Southern Thanalan. But as the way the OP mentioned, considering the rail line that exists at this stage is not particularly long, those ideas just won't work I'm afraid.

Still, any use of trains in this game I definitely support! (I'm like Selphie in that I love trains. ).