However, the values observed are given rather accurately by a theory that considers simply each atoms motion as a whole, assigning no internal motion to it.
A limit which is inherent in the nature of things and can never be surpassed by improved technique or increased skill on the part of the observer.
Questions about what decides whether the photon is to go through or not and how it changes its direction of polarization when it does go through cannot be investigated by experiment and should be regarded as outside the domain of science.
I disagree highly with this quote, though I accept from the literature/pedagogy that "hidden variables" are not at play/responsible.
The behavior of these photons represents the constructive and destructive interference resulting from the wave behavior of matter, where crests and troughs cancel out, and crests meeting crests combine.
The new theory avoids this violation by connecting wave functions with probability for a single photon, where each photon is partially within the beam components, and thus only interferes with itself.
The intermediate character of the state formed by superposition thus expresses itself through the probability of a particular result for an observation being intermediate between the corresponding probabilities for the original states 1, not through the result itself being intermediate between the corresponding results for the original state.
The probability of a particular result for the state formed by superposition is not always intermediate between those for the original states, in the general case when those for the original states are not zero or unity, so there are restrictions on the intermediateness of a state formed by superposition.