Sorry I know the title of this question is kind of weirdly worded, but it kind of takes context to understand what I'm asking better.
So my current understanding of quantum superposition is this: So when an electron is unobserved it occupies a superposition of all possible position states, essentially meaning it is everywhere it can be at the same time. (See: first few sentences of https://en.wikipedia.org/wiki/Quantum_superposition#Hamiltonian_evolution) However when observed it collapses into a single position with a degree of uncertainty (so still fuzzy where it actually is, just much less so.).
So imagine this scenario. An incoming photon approaches the electron. It can be said that when this photon interacts with the electron then the electron has been 'observed' and collapses into a single fuzzy position state. In some cases the photon is absorbed and the electron jumps up an energy level, and in others the photon is absorbed and then immediately rejected (non-resonant absorption). But either way most photons coming in are absorbed. But why does the electron take up a position by the photon, doesn't it have an equally likely chance of being on the other side of the atom, and thus not able to absorb the photon? But if that were the case the vast majority of incident photons would simply pass through materials. Most things would be transparent, but they're not.
So if the photon causes the position wave to collapse, then why doesn't it cause the vast majority of photons to not be absorbed.
Or I am completely misunderstanding the topic at hand?