BYU would be ranked MUcH higher even if they did just one thing and that is to disclose exactly how much money is given to BYU by the Church.
Another huge knock is the catagory Of percentage of students that graduate in 4 years which also relates to the percentage of students that end up graduating. These are very low for obvious reasons. Missions being one. The other being that many LDS get married at BYU and then that increases the likelyhood of dropping out due to pregnancy or just having to work or even sometimes dropping out/transferring because the husband either finds a job and they have to move or husband gets into grad school and they leave the area as well. While these things are logical and understandable, it hurts the rankings.
Also, BYU isn’t as diverse and doesn’t emphasis research as much as other highly ranked schools.