Energy and matter tend to be referenced as if the concepts are distinct--which is indeed the case--even by those who would say that nothing exists which is not made of matter. Ironically, the very energy featured in some scientific models, including some modern ideas about quantum physics, cannot be made of the matter it interacts with. One cannot prove anything more about the quantum world other than that nothing in it contradicts the laws of logic, but one can prove that certain conclusions follow from certain premises about quantum energy--including the fact that pure energy, if it exists at all, is by necessity immaterial.
For instance, the unverifiable tenets of string theory predict that matter is made of nonphysical subatomic energy, which would mean that matter reduces down to an immaterial "substance" [1]. String theory, if true (not that anyone can demonstrate it is true or false), would not have anywhere near the same kind of grand metaphysical ramifications if it simply posited that matter reduces down to more matter. That is the only option if matter does not ultimately consist of something immaterial! Of course, any existing subatomic energy could not be directly perceived because it would be the thing that undergirds matter, so it could never be directly observed or proven to exist when the senses do not perceive past the external world.
Science must study an immaterial thing like pure energy (or at least ideas about how hypothesized pure energy fits into a given scientific model) through observations of how it impacts matter. Pure energy itself is strictly immaterial, yet it could likely not be perceived by the senses if there was no materially detectable correlative impact of it on physical matter. Here, I am referring to energy in the way that some quantum physicists refer to the quantum world as a vast region of sheer energy, not in the sense of a comparatively mundane aspect of matter like the ability of a ball to continue rolling until it loses "energy" (i.e. momentum). Despite the fact that string theory's pure energy is nonphysical in a way that makes its existence unprovable, there are immaterial existents that are associated with science, albeit not in ways that many scientists ever seem to discuss, which can be demonstrated to exist.
Even if energy was just a manifestation of matter, meaning there would be no point in ever distinguishing between them at all, two things without which science cannot be conducted are immaterial in nature: the laws of logic and the consciousness of the observing scientist. Without the laws of logic, there could be no sensory experiences to process, for nothing can exist without logic--not in the sense that logic is just a description of whatever states of matter or mind exist, but in the sense that logic dictates what can and cannot exist in the first place. As for consciousness, one cannot observe the external world without a conscious mind which does the observing, and a mind is not identical to a physical brain.
One does not even have to go this far into the metaphysics of material and immaterial things in order to show that even seemingly naturalistic scientists might contradict their own philosophically invalid beliefs when elaborating on the distinction between energy and matter. Of course, the distinction between energy and matter would not refute all forms of naturalism. There is a difference between the form of materialism holding that everything at all that exists is physical and the form of materialism holding that whatever immaterial things exist cannot exist apart from matter--but both of them are easily falsified by the nature of the laws of logic [2].
[1]. https://thechristianrationalist.blogspot.com/2019/09/the-pseudoscience-of-string-theory-part_3.html
[2]. https://thechristianrationalist.blogspot.com/2018/11/the-ramifications-of-axioms.html
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