If that were the case, then any catch made with two feet in the end zone where the player falls out of bounds would be ruled incomplete because the player lands out of bounds. As soon as there is possession with the ball in the end zone, it's a touchdown-- provided the player maintains control through the ground. If he had dropped the ball as he landed, they could call it incomplete. But he didn't.
He had two feet, a knee, and the ball in the end zone at the time of possession. Anything that happens after that is meaningless as long as he maintains control.