When Congress passes a law saying, "create an agency that sets rules about air pollution, whose director is appointed by the president", the constitution demands that the executive branch do exactly that. Interpreting that to mean "The president personally sets rules about air pollution, using an agency if he likes" is unconstitutional and I think the vast majority of both parties agreed on this for most of the last hundred years.
If Congress disagrees they have ways to override the president. They can pass new laws or even impeach him.
But unless the dems get 2/3 the senate that will never happen.