Well, same reason I exclude anything else.
Think about it like this; when an atom moves, does the space move with it? No, the nucleons and electrons move through space.
But if you want to define an atom as being the space too, fine. It's as pointless as arguing over whether the definition of a cardboard box should include the air inside it. The air's still physical though.
And I should point out that saying that most of an atom is empty space is a misconception of the nature of an electron. In reality what gives an atom its large size is its 'electron cloud' which is a could of charge generated by the instantaneous displacements of the surrounding electrons resulting in a sort of overall smear of electron moments. The large sphere of space around the atom is not empty at all, but rather represents the zone in which there is a high probability of finding the electrons.
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