Each section (region) has their own way of doing things. Getting people accross the state to agree politically is a difficult thing.
Still is. You have schools of 4000+ racing from the Southern Section against McFarland that has 770 (also in D1). They should have about 6 more state titles and quite a few more state top 3 finishes. Currently their section put them in the highest division despite their enrollment in efforts of creating D1 as a "championship" division with the the best teams (most with 3000+ students). While a good idea this has kept McFarland from even making the state meet where they are a top 3 team for a school of their size.
The CIF has decided on a geographic state meet. Which is the right thing. But how do you do that fairly? So as you can see its a mess. Currently sections make their own rules for their sections and send who they want.