Makin this system dependent upon slower parts of the brain, such as the conscious thoughts, would likely decrease reaction times when you need it the most. Muscle memory and instinctual reactions access parts of the brain which are older and better connected to every part of the body than our conscious thoughts.
At the end of the day, even if the whole system could be linked to both instinct and wilful action without drawbacks, there wouldn’t be any advantages to it. People with such a “super system” probably wouldn’t pass on their genes anymore than their neighbors. Considering how genetics work, anything that doesn’t have a strong natural selection in favor of it tends to disappear or degrade fast after a few dozen generations.
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