Unlike the right to be secure in your effects, there is no constitutional right to buy a car with any particular characteristic, including a high level of emissions. Therefore the Feds have an important say in the encryption debate, but in car emissions, much less so.
Since the answer about CARB compliance isn't found in the bill of rights, it is just up to legislators to decide how they want to run their states. And from a practical standpoint, one can argue that non-CARB compliant cars cause bigger problems in large and dense cities. As a result, states with large and dense cities might conclude that the difficulties of making and distributing different versions of cars are more than offset by the benefits of lower emissions, while states without big cities (or lots of car manufacturers) might balance the scale in the other direction and allow higher emissions.
But even though you made a bad analogy, at least you made a *car* analogy and for that you should be commended.