In the purely empirical world view, a person is seen as just a "collection of atoms"
Actually, no. In pure empiricism the best you could do is say 'everything I have observed sufficiently closely has been made of atoms'. Unless the empiricist has observe all humans at the molecular scale they cannot claim that a person is 'seen' to be a 'collection of atoms'.
A pure empiricists that reasons that since everything they've seen closely is made of atoms, and since the theory 'everything is made of atoms' produces a coherent explanation that explains new things and produces predicts etc, therefore we can expect that person x is made of atoms...would be using rationalism plus empiricism.
. It fails, however, to take into account the complex emergent phenomena that make a human being so much more than "just atoms".
Emergent properties are just as observable (if not more so) as molecular ones. So no, empiricists would not fail to take emergent phenomena into account. Indeed - the observation of phenomena is their characteristic!
Have you confused empiricism with reductionism?
What does any of this have to do with Nohadism and theism?