It basically looks at the average across all majors. They're claiming that they compare across majors, but a simple glance says that's not true. BYU has more majors, including lower-paid ones. An example includes Communication Disorders Sciences and Services which is at BYU but not UVU and it has a low pay (lots of stay at home moms as someone else mentioned?). Also for some reason, BYU dance graduates ear less than UVU dance graduates.
A much better comparison would have been to look at the common majors and then compute the average. Salaries are also only calculated from students who had financial aid.