This dawned on me as well when I watched a Feynman video on electromagnetism. He talked about that you can explain the "how" of its working, but not the "why". The fundamental forces of the universe are basically magic fields. And this is true for anything that is fundamental and can't be deconstructed further into more primary components.
Layer one encompasses the physical layer so I'm not convinced there's an additional layer to be had. It does require a deep understanding of the physics involved though.
We have a clear and clean description of the apparent bottom layer of the universe, but we also have clear evidence that it's incomplete, that there's something else going on. So, physicists are spending billions of dollars trying to look one layer deeper and find "new physics." To no avail, yet...
