They have a clear advantage in being able to enroll students from across the Philadelphia area. Whether that is an unfair advantage depends on your perspective. North Penn has an advantage over most of its opponents in having quite a few more students. As Roxy pointed out, nearly all pubic schools--certainly the suburban ones--have better and much more convenient facilities than the Prep has. That's an advantage, but neither of these public school advantages seems unfair to I would agree that the Prep's geographical advantage is bigger than, say, the advantages nearly all public schools have with respect to facilities and the absence of any academic standards that would exclude certain potential students or prevent current students from being able to participate on a team. (I'm not saying all Prep students have to be candidates for the National Honor Society, but I am saying they have to achieve and maintain an academic standard that would not be a requirement for students in public schools to be "in good standing," i.e., able to play on a school team.)
What do you want SJP to do? Leave the PCL, where it's been a member since the league started about a century ago? Do you want the PCL to leave the PIAA because every PCL school recruits all its students, including, obviously, all its student-athletes? Do you want the PIAA to set up a separate classification for non-boundary schools, which may make no sense at all outside the Philly area? (Be careful what you wish for--consider the Jersey example.) Do you want the PIAA to exclude all non-boundary schools, including charter schools and all the (mostly very small) Catholic schools scattered around the state? Or do you want the PIAA to exclude only the PCL after inviting them in less than 15 years ago, even though the PCL, as far as I can see, hasn't done anything it wasn't doing when they entered the PIAA? Or do you want the PIAA to exclude just the SJP football program, even though it does nothing different from what LaSalle, Wood, Roman, O'Hara, PCC, Erie Cathedral, Bishop McDevitt, Shanahan, etc. are doing?