I guess some people use them that way (either just incorrectly, or in casual speech), but they aren't, really. Not even
according to Merriam-Webster, which is among the more "descriptive" (vs "prescriptive") English-language dictionary publishers, i.e.:
Code:
Fundamental:
1 a: serving as an original or generating source : primary
b: serving as a basis supporting existence or determining essential structure or function : basic
2 a: of or relating to essential structure, function, or facts : radical; also : of or dealing
with general principles rather than practical application
[...]
4 : of central importance : principal
[...]
"Simplistic" and "superficial"
are antonyms of "thorough" (with different shades of meaning), and relatively speaking (again, in the historical scheme of things) I think at least the former of those two would be a not-inappropriate word to describe our current state of knowledge of the "nature of matter and energy and the relationship between the two".