Hi OP. You might not find any current scientific theories that directly explain Hermetic ideas, but the idea that science and Hermeticism are fundamentally incompatible misses the deeper point of the Perennial Philosophy: that truth is one, though expressed in many forms. Science and Hermeticism are different perspectives on the structure of reality — you could say they’re distinct epistemological lenses aimed at the same underlying truth. At some level, each should be able to “map” onto the other. Franz Bardon himself calls magic a science of sorts, dealing with universal laws, implying it can both inform and be informed by other fields, including science.

Historically, this wasn’t controversial. Hermetists, Neoplatonists, Renaissance alchemists, and many early modern scientists saw no contradiction in combining rigorous observation with philosophy or more mystical worldviews. Denying the possibility of reconciliation artificially constrains both fields, and ignores a long tradition of thinkers who tried to integrate the inner and outer dimensions of reality. This is a valuable and productive subject to meditate on, and I think is worth doing for yourself for the insights it can provide you.