None of this is going to be rigorous or have a right answer, so please don't take it as though I'm demanding one. I'm just interested in everyone's thoughts.
It feels to me (and possibly you) that energy has a different ontological status than something like matter or light. If they are "first-order" it seems "second-order". While observing matter interacting with other matter, we realize that a certain mathematical quantity is conserved, which we call "energy". We then use it to great predictive effect. But it seems strange to then turn around and grant it the same kind of existence as matter -- it should be at a "higher level."
Of course, if you're asking whether something exists you're really asking "does it affect physical processes?" or "does it function as a cause of other physical processes?" My question is, does energy pass this test? If we observe a boulder falling from a height and crushing a village, at one level we could say that its potential energy was the cause, but at a lower level we could say that the pull of gravity on its individual molecules was the cause, and at a higher level we could say that the negligence of the boulder-watching crew was the cause. But we don't think of negligence "existing" as one of the primitive substances in the universe.
Can someone point me to a reference for prior writing or thinking on this?