I agree with you that most people who believe in souls identify with their souls rather than their brains, and it's not clear to me how any of what I said changes depending on whether people identify with their souls or their brains. But I'm also not strongly committed to this particular metaphor; if you have one you prefer, or have a different formulation of the argument in question you'd prefer to use that doesn't depend on metaphor at all, I'm happy to use that as well.
No plot spoilers here, just wanted to flag a bit of poor reasoning that shows up in Chapter 39:
This is a surprisingly common fallacy. Just because X depends on Y, it doesn't follow that X depends on nothing but Y. A phenomenon may involve more than just its most obvious failure point.
To illustrate: Suppose I'm trapped in a box, and my only way to communicate with the outside world is via radio communication. Someone on the other end argues that I don't really exist -- "There's no person beyond the radio receiver, for if there was then there wouldn't be any such thing as damaged radios!" Pretty silly, huh? But people say this kind of thing in defense of physicalism all the time.
(N.B. This is not to defend the existence of souls. It's just to point out that this particular argument against them is invalid.)