I'm no lawyer, so I invite any LAWYERS to correct me, but:

the supremacy doctrine is based on the supremacy clause of the Constitution, which was intended to reign in the Federal government, not authorize it to run roughshod over Individuals or states.

Supremacy Clause: "This Constitution, and the Laws of the United States which shall be made in pursuance thereof; and all treaties made, or which shall be made, under the authority of the United States, shall be the supreme law of the land; and the judges in every state shall be bound thereby, anything in the constitution or laws of any state to the contrary notwithstanding."

That doesn't mean that the Federal Government can make up any vile thing they want and call it the "supreme law of the land." The valid laws they make must be in pursuance of the Constitution.

Pursuance - the carrying out or pursuing of an action, plan, etc.

It doesn't make sense for an unconstitutional, unpublished rule or standard operating procedure of a federal agency to enjoy the protection of the supremacy doctrine with regard to correction from state legislation.