A-T theorists might be right that contemporary science does not register formal and final causes (though the mathematical character of scientific law is formal causality, so…) but they should be more interested and concerned in the far more significant fact that science does not register primary and secondary causes, whether agent/ instrumental, equivocal/univocal, or universal/particular. Identifying the primary/secondary relation was the whole point of pre-Galilean physics and it gave structure to the whole scientific procedure. Aristotle’s geocentric view of the cosmos, for example, wasn’t an attempt to map out the space of the cosmos but to articulate the orders of universal causes. He wouldn’t have seen figuring out our distance from the sun as a scientific triumph nor as playing a role in a scientific account of the world. Ditto for a precise mathematical account of the arc of a projectile. The point was to identify a causal chain of some genus, terminating in the universal cause of that genus.
Contemporary accounts of nature rule out the discovery of primary causes for two reasons: (a) mathematization requires that all events occur in a homogeneous space-temporal domain and (b) science sees its job as modeling interactive systems or at least as finding correlations of events that follow some algebraic law. The times when someone trained in A-T science might be tempted to find primary causes in contemporary sciences tend to be times when they are incapable of explaining what they means. Kinetic energy seems to count as some sort of universal cause of change of place, but the kinetic energy is not defined in a way that allows us to answer the question. since no one can say if it is just a mathematical convenience, a cause of motion, an effect of being in motion, or a dozen other things. Physicists do not regard it as a scientific question to wonder whether kinetic energy is in motion with the body it moves or whether it caused motion without being in motion, though this would have been perhaps the chief question that Aristotle would be interested in answering.
One response to this is that Aristotle asked questions that have proved intractable. The best we can hope for is a description of interactions and not an account of the being of things in a universal way, in the way that an artist explains not just this artwork but art as such. Nominalists might claim that these problems are intractable since there are no genera of things to serve as objects of action. This objection would conflict with science positing all sorts of unified genera (what else would force or energy explain?) though perhaps the incoherence we encounter in asking ontological questions about scientific objects arises in part because of this Nominalist presupposition.