In the past if you didn't want to play for school you had to get sign off form the school, which basically only happened if you were good enough to play Central League. I think that means the schools have always felt that they had "first dibs" on players. I'm not sure that's right necessarily and schools do have to move with the times, but it also seems that the academies aren't consistent with who they allow to play for school which makes the situation messy.
Schools still behave/bluster like this, but the reality is the education act doesn't grant schools powers over non-school extra-curricilar activities. They can be ignored.