According to FindUniversity.PH, the "Philippine Universities Ranking is based on the aggregated passing rates of each school in all board exams that their graduates participated in. It is the first Philippine Universities Ranking that is based on relevant, up-to-date and measurable data. There are over 60 different board exams conducted by the PRC, and we aggregated the results from those board exams, ranked each school in each board exam, and then aggregated the rankings for each school, to come up with a Weighted Board Exams Ranking for each school.
Note that the official ranking contains only schools that were ranked in at least 10 board exams."
(please note also that Thoughtskoto didn't rank these schools but only posted the result from FindUniversity)
Read their methodology here
Update: Searching at least 5 board exams in the list will put Ateneo de Manila at Top 3 and will put UP Visayas as No. 1 in Western Visayas Region)