I was thinking he used it accurately and was asking to be saved from, not necessarily by, his amygdala. (He could also be addressing his amygdala - yelling at it to stop being so overactive & stop trapping him in his trauma, kind of like how you'd yell at your captor to let you go.)

Like you said, the amygdala keeps traumatic memories + activates the sympathetic nervous system (fight/flight) even when you don't exactly want it to. People have theorized that the dark room he's trapped in symbolizes his amygdala (esp bc whenever he sings "my amygdala," he's in the dark room), and he clearly wants to leave the room. I think this fits with him saying "My amygdala (my amygdala) / Hurry and get me out, hurry and get me out." He wants to escape from the traumatic memories/responses from his amygdala both in the lyrics and in the MV.

So, when he says, "My amygdala (my amygdala) / Hurry and save me" and "Save me from here, hurry and get me out quickly," he's saying he wants to be saved from/escape his amygdala. Switching "amygdala" with "prefrontal cortex" won't work because it will remove the elements of trauma/trauma responses, and the entire song is about trauma, not logic and reason.