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MrShaggy comments on Inhibition and the Mind - Less Wrong
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"These points illustrate a very important basic principle: the mind is made out of ‘layers’ of modules and functions, starting with the most rudimentary, basic, and primitive, and moving to the most complex and subtle."
The evidence you gave doesn't point to this conclusion. Modules and functions are the dominate way of thinking about how the brain works currently, but what you've shown is only that the brain isn't a single process free of contradiction. More importantly, even in the view of modules and functions, the rudimentary/basic/primitive ladder to complex/subtle doesn't follow. Sure the front cortext is more recently evolved, but according to what measure is it more complex than another part of the brain? I could be wrong, but I think you're sort of anthropomorphizing parts of the brain (the reptilian part is primitive, the 'human' part is complex).
It directs, integrates, and regulates many of the other parts of the brain, and causes them to work together in particular ways or suppresses their output.
It is responsible for the complexity of what we regard as human behavior. The losses when this part of the brain is damaged are horrifying. Sufficient damage, and it is questionable whether the resulting creature can be considered 'human' in any meaningful abstract sense. (The biological sense is met, of course. But concepts like 'personhood' no longer seem to apply.)
Right, it's responsible for the complexity of what we regard as human behavior, but that doesn't meant that part of the brain is more complex than other parts. Also, I doubt but do not know that it's the only part that regulates or suppresses other parts.