You're missing a key component. Before the micro lens layer above the sensor, you really did miss light with more pixels, as some percentage of light fell between the photosensitive parts of the sensor and was lost. This likely still happens with the micro lenses, but to a lesser extent.
Despite the micro lenses, which I believe my 7D2 was one of the first to get the micro lens treatment, and the level of visible noise at ISO 100 on a 7D2 is surprisingly visible. That noise exists, and didn't on my 7D. With micro-lens and only a minor resolution bump that absolutely shouldn't be true... but it is. If it isn't the smaller pixels, where is this noise coming from? The fallacy may be what part of the process the noise is being attributed to, but the extra noise IS there.





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