Can kind of see where IHSA is coming from. Take the school's enrollment from when the varsity team (mostly made up of juniors and seniors) were freshmen and sophomores to get an idea of where the team - not the entire school - fits in for the upcoming two years. Especially in football, where freshmen and sophomore contributors are rare, seems like a decent way to get a snapshot of where the team fits in. If you just took STL's enrollment from this year, you're taking into account much larger freshmen and sophomore classes, 99% of which are not contributing to the varsity football team. Not perfect, but I understand it.
DePaul and STL are anomalies - rarely are you going to have schools (especially Catholics) that have spikes in enrollment like they have had that provide bad optics for sports classification. In STL's case, junior and senior classes are much smaller than freshmen and sophomores and next year's classification will reflect that. It will level off soon, at least for STL who wants to max out at 1200. Not sure what DePaul can grow to.