Think in terms of a layered system (subsumption architecture is useful [1]).

Sure the substrate is the brain and is common to all layers, but the layers are functionally different.

The self-model, "you" is a high-level circuit. The low-level circuits make all decisions and relay the results to the higher levels.

[1] https://en.wikipedia.org/wiki/Subsumption_architecture

[2] https://www.rifters.com/crawl/?p=9000

From your second link: "Will and perception do not cause the firing of neurons; they result from it. By definition, everything we are conscious of has to be preceded by neuronal activity that we are not conscious of. That’s just cause/effect. That’s physics."

I guess that is the part that I have trouble with... especially the first sentence: ""Will and perception do not cause the firing of neurons; they result from it"

They don't cause it OR result from it... they ARE it. Everything that is us (including our free will) is made up of those neurons. Our thoughts are neurons firing. Everything we think and believe and experience and decide is contained in those neurons, their state, and their connections.

I always thought the question of free will (at least since I was a philosophy undergrad) was about whether our brains (and the universe) are deterministic or not. I feel like the more we learn about quantum mechanics and physics, the more it seems like the world is NOT deterministic. The uncertainty of the universe means the neuron behavior is NOT deterministic, and that non-determinism is where free will lies.

The neat thing about layered systems is that they don't really exist. The sin of the "layering violation" is everywhere.