Dear Stephen,
You give very good doubts in the spirit of Descartes. As Hegel said "The owl of Minerva begins its flight only at dusk."...To overcome the modern crisis of understanding in the philosophical basis of knowledge today, mathematicians and physicists must stubbornly "dig" to the most remote meaning-distinguishable ontological depths. Carlo Rovelli is right: Physics Needs Philosophy / Philosophy Needs Physics . The same can be said about mathematics, taking into account the centennial problem of the "foundations of mathematics", which Morris Kline well presented in "Mathematics: Loss of Certainty": "Mathematics needs Philosophy / Philosophy needs Mathematics".
From the list of Carlo Rovelli the most pressing questions for modern physics, the first two: "What is space?", "What is time?". Therefore, the conclusion: Mathematics, Physics and Ontology must meet each other and meet at the ontological "point with the embryo of vector". Here, the dialectical ideas of Kuzansky and Whitehead (process metaphysics) are already helping.
Planck and Einstein began more than a hundred years ago the Big Ontological coup in the foundations of science. But this coup was not completed. Any theory that claims to be fundamental must have an ontological basification (justification substantification). Quantum theory and General relativity are phenomenological (parametric, operationalistic) theories without an ontological basification. Therefore, it makes no sense to combine them, let each work on their own "field". Today, in order for science to overcome the crisis of understanding, the holistic paradigm - Universum as a whole - must come to the aid of the paradigm of the part.
It is necessary to start an "ontological attack" on "matter" with the goal of its deeper, holistic, understanding in the spirit of Plato: matter is that from which all forms are born. This is also required by the modern Information Revolution and the solution of the problem of the nature of the phenomenon of "information", its place in the scientific picture of the world. Let us recall the ancient Greek "goddess of form" Eidothea, daughter of the sea deity Proteus ("Proteus of nature" is a metaphor for "matter") and the goddess of the sea sand Psamata, who told Menelaus how to put Proteus on the net so that he could tell Menelaus the way back to Greece ... Concepts "dark matter", "dark energy"- entities without necessity. In order to "grasp" (understand) the ontological structure of matter, the "Occam's razor" must be extremely sharp. To understand is to "grasp structure" (G. Gutner "Ontology of mathematical discourse"). Criticism must begin from Newton's metaphysics - "Absolute space". Of particular great doubt is the philosophically naive hypothesis of Big Bang. At the same time, remember the philosophical testament of Paul Florensky "We repeat: worldunderstanding is spaceunderstanding."
Sincerely,
Vladimir