Good point. The Constitution requires only that nine States ratify it, in order to become operative. Fortunately, as Madison was discussing with others, all 13 eventually ratified, sidestepping a major constitutional crisis in which nine states would thenceforth be bound to one another by the Constitution, and the other four would continue to be bound to one another and to the nine by the "perpetual" Articles of Confederation, with a completely different (because truly federal) form of government that had no Executive or Judiciary.
Now that would have been interesting to contemplate, and supposedly Madison did lose a little sleep thinking about the possibility.
But as you say, from the moment the ninth State ratified, the Constitution came into force......without the other four States, who were still outside it, and under the Articles.