That rule in FL, to my understanding, is to prevent "clubs" from forming school based teams to get around practice/play limits. The key in that one is the "affiliated" term. It would not prevent players from playing on an ECNL team that has nothing to do with school.
Just cause everyone in Green-Spart-villburg who plays school soccer is on a CESA team does not mean CESA is part of the school system, yet....

Of course when they start the CESA magnet school things might require a rule like that