Atom does NOT mean indivisible (and I can't see how something indivisible is automatically immaterial, anyway). In fact, atoms
can be divided (nuclear fission, anyone?)
Atom is the basic unit of matter. That means
atoms are matter, so they just can't be considered immaterial. Atom being
is senseless. And it is not only the fact that they're material. "Manipulating the dimensions" and everything else in the description of aether is completely incompatible with atoms.
Believe me, you will not want to discuss physics with me.