I would say that it has everything to do with travel and time away from school. With finals, AP ect. imagine if they seeded the tournament and you were a team from western NY and you played Suffolk in the first round went home and had to come back three days later to play Nassau and go home and come back and play a State Championship at Hofstra all while finals and testing were going on.
The rest of NYS has to deal with all of the issues you've raised - NYS is fairly large state.
