Perhaps it's because universities have a limited number of spaces that they would prefer to give to successful students and truancy may correlate with success.
Not really. Japan currently has a problem of more spaces than students (aging population and all that). It is not as bad for universities as it is for elementary/high school, but it is a serious problem.
Or it may be that some classes require a team effort and truant students disrupt that (but for whatever reason, the team is reluctant to report it.... or it counts against them anyway).
This is more likely. I have TA'd for a course where the entire team's grade was determined by each member's assignments.
Anyway, I find this article highly irregular. My experience is that japanese universities will bend themselves backwards to prevent any undergrad student from not graduating. Also, all cellphones here
have GPS, not only iPhones. I think it is more likely, from RTFA, that the university is putting on a course for the students to hack with the iPhones, and the writer of the article decided to capitalize on the minor point of "trying to check attendance with the GPS".