The depots for this train seem to be in areas that are much more populated (Wikipedia says Mitaka and Toyoda [0]). If Otsuki Station is the station of despair, this would suggest the trains ride empty from Otsuki to the depot. Why couldn’t they allow passengers on that final ride to the depot, requiring them to disembark at Mitaka/Toyoda at the latest?
Otsuki might still be an booking-on/-off point for train drivers, with a number of drivers based there and regularly starting and ending their turns at that station and presumably living nearby. Or alternatively the train company finds it more convenient ferrying the driver with a taxi or company car to from the regular booking-on/-off point.
[0] https://en.wikipedia.org/wiki/Ch%C5%AB%C5%8D_Line_(Rapid)