> Material is mostly vacuum

This is not true in quantum physics. This is a big misunderstanding among many physics students that they live with for many years because they first learn about the atom using the planetary model of atom. In the planetary model the atom looks mostly empty. But this view of the atom becomes nonsense after learning QFT.

The space within an atom is filled with the wavefunctions of the electrons. If you still ask "but the electron is still going to be somewhere", I can only say that our intuition about classical physics fails in the quantum physics.