There are a few posters here who get very upset when the rules of the game are not followed by the organizers, but it happens and often.
The Japanese Federation, like ALL Federations are very protective of their appearance. They knew the new system of the quali round and knew one of their top skaters had to qualify a third skater for Japan - not for an individual (as Mrs. P pointed out). It's strictly Federation business. So they announced the Team for 4CC minus Oda. He obviously will be at the quali round.
It's all about a Federation which cares about a Team being strong.
I believe they could have sent Hanyu to the quali and Oda would be left out of the Worlds. NO? Who would object officially?