The courts take existing laws and regulations and try to make them fit, and different courts come up with different answers because the laws they're using never imagined this precise scenario.
Ideally we'd have a functioning Congress that would debate these issues and write carefully thought-out laws to regulate app stores. Until then, we just get messes of seemingly contradictory rulings that seem to be decided more by chance than by any clear cohesive principle.
In other words -- blame the legislature, not the courts.