People have to remember that the stipend amount isn't established by or for athletics. In determining a school's total cost of attendance (for general student population financial planning/aid purposes), there are four factors: Tuition/fees, Room/board, books, and transportation/personal expenses. NCAA scholarships traditionally only paid for the first three. The stipend is simply the fourth transportation/personal expenses line. This varies across schools for various reasons. It could be transportation costs to and from campus (which is likely why PSU's is a lot higher). It could be anticipated health care costs not covered by a student medical plan. Plenty of other things, too.
I've seen some articles suggest some schools could try to influence this value. I just don't see it. Schools don't want their total cost of attendance to increase as it could steer away the students that actually pay tuition.