Physics postulates a world explicable under the category of measurable quantities. Any such quantities it finds will be deemed "physical." The fact that everything physics finds is explicable in terms of the physical is not a hypothesis that physicists are testing, it is an assumption of their science.
As such it is ridiculous to point to the work of physicists as "evidence" for a philosophy which one may refer to as "naturalism." It is not a flaw of physics or physicists to make this assumption. What forms any particular science is the set of postulates which it makes about the world, and through which it proceeds to investigate the world as it is seen under those postulates. But it is a mistake to forget that these are postulates and not discoveries.
Consider an episode like the discovery of the weak nuclear force. Certain measurable phenomena cannot be explained through any of the other known forces. These phenomena have weird characteristics: certain parities that are usually maintained are violated, and quarks change their flavor. So physicists postulated the existence of a force that would produce these phenomena.
Now perhaps what was "really" going on was the God, having nearly finished creation, thought to himself, "I can foresee these people called physicists, who are going to think their theories explain everything. So let me continually cause the universe to behave in such a way that certain parities are regularly violated, and quarks change their flavor. That should shake them up."
So long as God did this in a measurably regular way, what we would see would be no different than if these things are caused by a "weak nuclear force." But physicists proceed by postulating things like heavy bosons and a weak nuclear force. One may protest, "But physicists are able to draw new predictions from their idea of these phenomena arising from a force!" That is great, and it is why physicists should continue to postulate forces. But the end result is not distinguishable from a case in which God was "fiddling" around with things in a regular, predictable way that hinted at further regularities to be detected.
Or consider the partial confirmation of Bell's theorem by Aspect et al. One might view this result and conclude, "Well, God just keeps these spatially separated particles correlated." But what many physicists have decided is that "local realism" is false. Now, local realism was a linchpin of the very idea of a "physical world," which is why Einstein and his colleagues proposed their original thought experiment, intending it as a way of showing that quantum mechanics must be incorrect in some way. But in the face of Bell and Aspect, what most physicists have done is simply to alter their idea of what "physical" reality is like.
Once again, I am not criticizing physicists for proceeding in this fashion: this way of proceeding is the very thing that creates physics as a distinct world of ideas. What I am pointing out is that is no more significant that physicists find everything in the world of physics explicable by physical principles than it is that Swahili speakers find everything in their world adequately described in the Swahili language. Swahili is, I am sure, a fine language, and I bet it describes the world quite well. But it would be a terrible error to leap from that fact to the conclusion that the world is actually built out of Swahili words and phrases.
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