For instance, Strominger/Vafa used string theory to calculate the Bekenstein/Hawking black hole entropy. Another example was Einstein's pulling Riemannian geometry off the shelf to describe general relativity. Communications and computer technology is proof of Shannon's Mathematical Theory of Communications. And there are many other such examples
In fact, the whole issue of matter itself is quite up in the air in physics. The Standard Model requires the Higgs which has neither been made nor observed. Even if CERN finds it, it would still be only 5% of the critical density of the universe. Hence all the work on supersymmetry because higher mass particles are necessary to explain dark matter (25%) which is the non-radiating form around which galaxies rotate and dark energy (70%) which is dissipated throughout the universe and acts a counter to gravity.
The mainstream of physics is looking to dimensionality (geometry) for explanations of matter.
Right, but the existence of the Higgs boson is, in principle, testable, and it's existence is expected to be confirmed or disproved when the Large Hadron Accelerator comes on line.
The mainstream of physics is looking to dimensionality (geometry) for explanations of matter.
As I said, induction and deduction can lead to the development of testable hypotheses. But the scientific method ultimately depends upon empiricism. Otherwise, we'd have nothing in the 'real world' to confirm or disprove hypotheses, and science would once again be nothing more than a branch of philosophy. The standard model is powerful precisely because it made testable hypotheses which have to this point been experimentally confirmed. Is it the last word on fundamental particles? Probably not; I fully expect a more simplified theory, which better explains the evidence, to emerge eventually.
It would look like Shannon's mathematical theory of communications, Einstein's special and general relativity models, Hilbert space, Godel's incompleteness theorem and so on.
Insofar as they present testable hypotheses, they are not "non-physical". Insofar as they are non-physical, they do not present testable hypotheses. You are talking about the borderline between mathematics and science. It may be a short step across, but there remains a distinction between scientific and mathematical knowledge.
In short, science cannot be rid of methodological naturalism, because that is what science is. When you begin seeking non-physical or supernatural explanations, you have entered the realm of mathematics or philosophy, and are no longer doing science.