Hi! I didn't try this program but I arrived at pretty much the same conclusions: after eliminating body burdens find out why my body overreacts do much. Turned out I had been in Fight or Flight my whole life and others were not (this was news to me)
The cause lied in bad initial instruction of my nervous systems. As a newborn I was not being held and was left to cry myself to exhaustion. My body learned from this that it is never safe, it lacks a basal safety modus and is on alert all the time.
Please not this is not a sob story but an analytical explanation of the system involved.
Turns out my body is more sensitive than of other people which is why my reaction is over the top. (Adrenal Fatigue after 35 years of F&Flight. Just at that moment when all your endocrine organs are slowing down and, as a female, the adrenals have to pick up progesterone production from the ovaries. Which didn't do a good job in me to begin with)
So: bad basic instruction of the parasympathetic nervous system + sensitive person + progesteron shortage + ambitious upbringing + life events = adrenal fatigue.
In my case.
It took me one year to wrap my head around the hormones. Another year to fix my digestion (high fat low carb and no raw foods or nuts or gluten. have to lay flat 45 after eating otherwise no uptake of nutrients. Use stomach aids -acidifiers- and supplements.) A third year to fix my sleeping pattern. Which was related to the amygdala system you talk about and/or the Fight and Flight modus I talk about.
As I believe the body is a flexible system and you can retrain it this is what I did, without help. First my body was as a scared chld and I talked soothingly to it. Aknowleding its fears and showing it was ok. I stretched and yawned a lot as tis aids the lymphe system to shed its waste. As does full fat foods.
I just kept telling myself I was safe over and over again. Used predictive math: "based on all the nights ypu have been safe before, what are the chances something happening tonight?" (robbers, fire, explosion)
I wear earplugs through the nigth as I find out my body only relaxes when it is silent. I wear them a few hours during the day too.
I follow what my body tells me. There are some ridiculous things my mind scoffs at but my body has a problem with them so I just follow: taking a shower makes me very tired. Garlic makes my hyper. Vanilline makes me crazy. If a drafthits my ankles I sneeze 7 times. I like a hood over my head.
I am not arguing with my body over these things, I just avoid them.
I have now recovered a great deal from A F. I was at a functionality of about 20%. now I am at 40%
which still is not much of a life. But I am much happier now that I am not in Fight or Flight all the time. You do know the opposite of it? It is Rest and Digest.
I feel further healing, in my case, has to come from pure adrenal and ovarium medicine. I think these organs are failing and am seeing experts (endocrinologist, who are only used to full blown Addison's and cringe at 'female problems' and I have neither of them. Still looking for an expert that will look at the whole system)
But yeah, amygdala, nervous system, Fight or Flight, I think it has a lot to do with Adrenal Fatigue and, like your post, they can be linked through basic explanations of the biological system.
One weird thing in this is how the biological system affects the moods of a person. Brain chemistry is a tricky thing. Various shortage will induce various moods in me WHICH AREN'T ME. It took a while to wrap my head around this and truly believe it. I can now distinguish between various moods and their dietary causes. I supplement accordingly.
In this, I do bring a wedge between my mind and my body.