“Is the “fight or flight” response the functional part of the primitive/reptile brain or the emotional brain?”
These distinctions about the brain – fight or flight response, primitive/reptile brain, emotional brain – are used a lot these days, but they’re inherently fuzzy.
The amygdala (as you know, there are two of them, one on each side of the brain) does initiate the fight or flight response through inputs into the hypothalamus (triggering the hormonal part of that response) and to brainstem control centers of the sympathetic nervous system for the neural parts of the fight or flight response. Some aspects of this response are emotional but some are not; and, complicating the distinctions further (among the fight or flight response, primitive/reptile brain, and emotional brain), some emotional shadings the amygdala is involved in don’t activate the fight or flight response (for example, the amygdala is involved in positive emotion processing), and some of our emotional life (“emotional “brain”) don’t involve the amygdala. See the complexities, here, in terms of the categories?
Plus, reptiles have a functioning basal ganglia, which is part of the subcortex on top of the brainstem and very involved in motivation and to some extent emotion; and, in the brainstem, there are nodes that can produce rage and fear, as well as nodes with oxytocin receptors (social system). The brainstem participates in emotion, and the so-called reptile brain is more than the brainstem: more complications. Also, the cortex is very involved in emotion, it’s not just the subcortex and brainstem: complications cubed!
“Amygdala hijiack” just means that the thalamus inputs into the amygdala with sensory information (carrot! stick!) which arrives before those inputs get to the prefrontal cortex. So the amygdala gets a second or two head-start over the cooler reasoning processes coming down from the prefrontal cortex. Also, more generally, the brain as a whole participates in “emotional hijack” that goes beyond the amygdala alone. The amygdala part of the emotional hijack is often overstated: it’s just a small head start. Still, in cases of prior sensitization of the brain due to trauma, that head start could make a big difference.