The chairness is not in the atoms, but in the form and function of the thing that they compose, and the reality of its form and function cannot be reduced to the atoms. Knowing only about the atoms doesn't let you point to chairs or talk a out how to use them.
The "undifferentiated matter" is just the collection of atoms in the universe without trying to classify them into objects. The classification into objects is done in the mind (and the way the atoms clump together in our universe makes this job very easy, thankfully)
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It's not atoms, because you can differentiate atoms out from the rest of the matter. Atoms are as in-your-mind as chairs are. Atomness is still x-ness for some x which is always interpretation and always in the mind.
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And you can't swap atoms with something else because that will still be x-ness whose existence is established by our experimental procedures upon the world. We can also never be certain when we hit bottom. Chairs to atoms is a continuum, physics isn't a separate magesterium.
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