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.
The Constitution gave Congress the power to establish uniform rules of naturalization and uniform bankruptcy laws. Neither power was exercised immediately; the first federal naturalization law was not enacted until 1790, and the first federal bankruptcy law was later. Until Congress acted, the states’ laws continued in force— not because the Articles of Confederation trump the Constitution, but because the Constitution did not prohibit state laws on these topics unless Congress chose to occupy the field.