Here is the waiver you are talking about:
The Clean Air Act allows California to seek a waiver of the preemption which prohibits states from enacting emission standards for new motor vehicles. EPA must grant a waiver, however, before California’s rules may be enforced.
The Clean Air Act itself provides a process for which a state may apply stricter
Clean Air standards for new cars than the Federal law allows.
If the Federal Clean Air Act did not provide for an appeals process to get a waiver, and the Federal government simply decided not to apply the law in California, you might possibly have an argument. But here, California is simply following the Federal law and using the appeals process that is in the law itself.
It should be pointed out again that this waiver only allows California to apply Clean Air standards that are stricter than the Federal law, not less strict. So the people of California are protected more, not less, from dirty air coming from cars than the rest of the country. I would also point out that, due to the famous smog in Southern Cal, California has had stricter state Clean Air laws than the Federal laws since at least the 1970s. They probably put the appeals process to allow stricter Clean Air standards in the Federal bill because otherwise all the California legislators in Congress would vote against the bill if it wasn't there. And California has over 10% of the legislators in Congress-the bill would have a lot of trouble passing if all the California legislators voted against it.