So there are two things we should identify separately that go under the name "quantization".
One is that when we send out a single photon worth of energy, even in an isotropic or other multi-path emission pattern, we only ever seem to detect a single photon. You can prove this with a half mirror and two detectors. This is kind of weird - not clear how this works, and the core question driving different quantum interpretations.
Second is that the energy level of a single photon detection is based on the constraint that Et=h (t is period), also written E=hf. This is not related to atomic properties of the detector. Why? Equation does not depend on any variable of the detector.
Same goes for Px=h. (Momentum/wavelength relationship.) You can prove that one with two razor blades close together. Same relationship, but along space axes instead of time.
Also for uncertainty principle - reinterpret EPtx as the variance of their distributions.
All of this is some sort of fundamental constraint of the universe around quantities of dimension force*time*distance (action). Not related to atoms per se. Not that I understand why this constraint exists. I know some ways to think about it mathematically, but not intuitively.