Before, I thought of meditation as a mental and emotional exercise. The physiological symptoms I viewed as secondary to these. The biggest shift was realizing that the deep purpose of mindfulness meditation isn't to practice being calm. While that is a benefit, it isn't primary, but is a side-effect of what is actually happening.
When something unpleasant happens to us, we feel it in our body. We develop a verbal thought about what happened in an attempt to describe it, and we generate a picture in our mind's eye. Then we forget about it. We distract ourselves with entertainment, or drugs, or reddit, and it goes away. Or so it seems at the time.
But around day 7 I had an epiphany as to what was really happening. When something negative happens to you, it's stored in your mind and your body(somehow). When it's stored it is stored at a particular level of emotional strength. When you remember the memory, it recreates the feeling, and causes you pain again.
There is a natural system for purging these pains in the body. Primitive human societies had far less stressors and distractions than we did, so when something bad happened, you had more time to heal. We don't have that now. We are constantly piling new things on, whether positive or negative, that distract us from the pains we have been through.
This disallows the physical systems that are in place, designed to clear psychological pain out, from working effectively. These pains remain stored in the body, and manifest as generalized anxiety, depression, etc...
When you meditate, you're entering a state in which your body can begin to naturally clear out the queue that has built up. However, this isn't necessarily obvious. The ten days lets you really have time to dig in and get things cleared out.
This queue is fairly obvious when you spend the ten days meditating, because every painful thing that has happened to you, starting with the day before the retreat, bubbles into your mind, and then works backwards in time. If you face the memory without responding, the next day you wake up and it carries no emotional weight. Everyone at the retreat had this experience. No one expected it.
There came a time near day seven when I realized that the emotional memory was stored in these pains and knots in my body, that I would do a body scan of a particular part of my body and ask "what are you?". Floods of memories would come out, along with the pain attached to them, and I do my best to face them without reacting. The next day the discomfort in that area would be gone. Remembering the memory would produce no pain.
There is a neurobiological explanation, which is that every time you remember something a copy is re-saved, not the original memory. Each memory has at least three attributes - verbal, visual, and emotional. When a memory is brought up, it is brought to your awareness and you are given the opportunity to re-save it with the emotional weight you now think it deserves. If you panic it is saved with higher emotional weight, if you stay calm it is saved at a lower emotional weight.
tldr; Mindfulness meditation facilitates a natural physiological process designed to help your body cope with and clear out emotional pain linked to memories. If this process doesn't happen it will cause generalized emotional distress in the form of anxiety, depression, neuroticism, etc...