Question: What happened to the real Sean Fentress?
Answer: He died in the train bombing along with all the other passengers. If you're asking what happened to the real Sean Fentress in the alternate time line created at the end of the movie, Colter took over his body and continued to live the life that Fentress had been living.
Chosen answer: Trains that shuttle back and forth on shorter stretches don't usually turn around at the terminus. They simply go "backwards". So, in one direction the loco is in the front, on the way back it's at the end of the train.
Ioreth