Actually, Ken does support box theory.
The idea is that both sides have 36, leading to a total of 72. Because characters are split into the "groups of 9", like Mario through Pikachu with Dark Samus, for them to line up correctly there would have to be an echo fighter between Palutena and Cloud for it to line up the way the placeholder looks.
Basically, we'd have to get Medusa, Zack Fair, Celica, Ms. Pac-Man, a Shulk clone, Bowser Jr. clone, or a Duck Hunt clone. Or Ken.
That's why Ken could conceivably add credence to box theory. But he alone doesn't prove it.