Under the Articles of Confederation, anyone naturalized by one of the States became a naturalized citizen of the United States. States continued to naturalize citizens of the United States even after the ratification of the Constitution, until Congress passed the first federal naturalization law in 1790. Someone naturalized by, say, the State of Virginia in, say, December of 1789 was a citizen of the United States but not a Natural Born Citizen, and not eligible to be President.
Your saying, that the "states", under the Articles of Confederation...AFTER the Constitution was ratified, were naturalizing citizens as citizens of the United States (and not "just" in their state)? That, it would seem, in effect means that the Articles of Confederation trumped the Constitution as federal law.