What scenario is avoided because the Constitution contains the supremacy clause

Well, for one, if California decided to pass a law that limited the President of the United States to only one term so that President Trump can only serve four years the supremacy clause would be invoked because of the already implemented 22nd amendment only allowing 2 terms. So to answer your question, a scenario that would be avoided would be if the state is purposely trying to "destroy" the federal government.