Each division has 5 teams, and plays each other more often than other teams. Divisions as they currently stand basically have no meaning in the current NBA. The in season tournament seems like the perfect opportunity to use divisions, as they play each other more anyway and it means less travel, and each division would have at least one representative in the next stage.
Competitive balance. Imagine how insane the Pacific division group would have been last year.
The hope is for the 4 best teams in the conference to qualify for the KOs. If three of those are in the same division, it becomes impossible for all 3 to qualify and some mid team from a weak division gets in.