Consider also the energy it takes to do those maneuvers. And that the station needs to be maintained; even though it doesn't seem to be staffed, the cost of keeping it in shape over many years was likely nonzero. I am not a train expert, but I suppose that stations require additional infrastructure - like lights and semaphores - which also needs to be maintained and regularly tested. Then you can start pricing in the opportunity cost of the land that could be sold or put to different use. And the organizational overhead of adjusting schedules to match the girl's lesson plan. It adds up to some considerable costs, of which the company management was surely aware...
...and yet they chose to ignore it. That is indeed just beautiful.
They were already paying it though. It wasn't an additional cost they had to make. It was a cost they chose not to cut for a period of 3 years. I agree with you, it is beautiful.
Technically it just says the station is closing. It's possible the line will remain operational. (The train might be going by there anyway.) Although it did say the schedule was adjusted for the student, so maybe not.
Edit, ah, so I guess a bunch of trains go by, and adjusting the schedule basically means deciding which trains stop at that station, not changing when trains run.
Looking at Google Maps the change won't be terribly drastic in reality [0] unless the station just over 3 km further down the line closes too. For a person walking it's a decent distance but for the rest of the passengers there would be very little change. Of course the same could be said for pretty much any station that closed between there before now.
Unfortunately my source is second hand as well from a Japanese discussion thread, so my information may be faulty.
One possibility is that the station 3km away is already out of operation (and I do recall someone posting that a nearby station did already shut down).
In either case I think you are right that for 99% of the passenger life will go on as it always has.
When I was little I lived in the country for a while. I was the only kid at my stop. But at least when I got on the bus it was full of other kids, most of whom were also the only kid at each of their stops. This girl is the only person on the train.
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.