The outer orbital is being treated as the last layer of an onion and the atoms are "inside" that. But orbitals are not spherical so our geometrical intuitions kinda fail.
Edit: Sorry for unclear wording: well, s-orbitals are spherical overlapping probability clouds, but they are not shells like an onion. Nor are they spheres as we commonly think of the geometrical object. To say something is "inside" a probability cloud gets difficult. Disclaimer: my memory/understanding of physics/chemistry/probability is poor. Edit 2: when orbitals of atoms overlap for molecules, don't the orbitals get funkier shaped probability distributions? Surely the same thing happens here and the cloud shapes would change - orbitals are not independent things you can just smoosh together or overlap willy-nilly due to qwuantum blah blah.