Earlier quoted context omitted.
I don't think that the article implies anywhere that this girl is the only person on the train . She is just the only passenger on her station .
Maybe something is being lost in translation, but the article starts with: "The train makes only two stops—one when a lone high-school student leaves for school and the other when she returns." The train makes two stops, rather than "the train stops here only twice". Both may be true, but the initial statement describes actions of the train rather than the station.
"The train stops there only twice a day—once to pick up the girl and again to drop her off after the school day is over."