What do you mean by 'metaphysical' here? I'm under the impression that metaphysics is a pretty deep branch of philosophy -- more like Descartes saying "how do I know I can know things", less like us saying the physics is probably magic. You seems to have landed on a particularly intense form of relativism, which is a fine way to run your life, particularly if it leads you to be open to the experiences of others. But I think it is different from metaphysics (although I'm not very educated in philosophy, generally).
With respect to atoms -- the standard of 'realness' science seem to use is whether we can make reliable predictions about the behavior of a thing, and atoms seem to have put quite a few points up on the scoreboard compared to the woo-woo stuff. Now, if a real philosopher were here they'd probably point out that all of science suffers from the 'problem of induction' and that gathering a preponderance of evidence doesn't really prove anything, but c'mon we're mostly engineers at best here. Our models aren't wrong, they are just limited to a subset of the entire universe of possible phenomena (the ones people will pay to exploit, obviously).
With respect to atoms -- the standard of 'realness' science seem to use is whether we can make reliable predictions about the behavior of a thing, and atoms seem to have put quite a few points up on the scoreboard compared to the woo-woo stuff. Now, if a real philosopher were here they'd probably point out that all of science suffers from the 'problem of induction' and that gathering a preponderance of evidence doesn't really prove anything, but c'mon we're mostly engineers at best here. Our models aren't wrong, they are just limited to a subset of the entire universe of possible phenomena (the ones people will pay to exploit, obviously).