The Ghost of Caravaggio
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According to empirical results, ISO 100 results in a higher dynamic range....
Am I better off (in terms of dynamic range) setting ISO 100 manually?
In general the purpose of automated camera settings is convenience. The people who designed the automation algorithm were at an extreme disadvantage. They have zero knowledge whatsoever about the actual circumstances faced by the photographer. It can be a risky to delegate camera setting decisions to people who have no idea about the actual challenges you face. The more challenging the situation, the less useful their uninformed guesses become.
In your case, it appears the goal of auto ISO is to intentionally underexpose the sensor by 1 stop (camera ISO setting is set to one stop above the sensor's native setting). This protects inexperienced photographers from overexposing the sensor (it does not protect them from clipping the ADC!). Still, this goal increases the chance inexperienced photographers will be happy with the camera.
But your goal was to make full use of the sensor's analog dynamic range. Your goal and the product design goal were in conflict.
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“…the mathematical rules of probability theory are not merely rules for calculating frequencies of random variables; they are also the unique consistent rules for conducting inference (i.e., plausible reasoning)”
E.T Jaynes, Probability Theory: The Logic of Science




