What you call configuration is what I call the chemical composition or matter spectrum of an object. An object is a superposition of actions of matter and those actions involve the elements and chemical compounds as well.
You are correct when you say there is more than just matter and action. There must be another axiom to close the universe of matter and action and the emergence of time and space from matter and action are exactly what close the universe. In fact, just matter, action, and time are sufficient to predict the actions of all objects.
How actions create an object of matter is certainly part of the story and a matter spectrum in principle completely describes each object, what you call a configuration. In fact, our consciousness measures a kind of crude matter spectrum for each object that we perceive and that is how we predict action. Science has even more elaborate matter spectrometers and therefore science has even more precise predictions.