^^ Circular reasoning. Assumes that reason and intuition are non-physical. And then even contradicts itself by pointing out the physical causes for the former.
The article I linked to only describes how the logic circuitry occurs by way of electrical activity around the neural networking. That is the physical/material activity; electricity and secretions. If not a separate mind, what is performing the actual logical functions. In other words, think of it this way - if the mind were not separate from the brain, why would the mind be aware of anything other than the brain? It would seem that there must necessarily be something other than the brain to turn the neural activity into logic and reason.
I think this is badly stated, but you are voicing ideas of consciousness which are supported by Deepak Chopra, and other New Agers, so I will use their idea as basis for this reply.
They turn the [human] brain into a kind of remote control receiver. So, a super complex "soul" exists outside the physical plane brain, in a more powerful realm, say the Astral plane. Others build on this, and have a soul plane. This means that the brain is supposedly, mostly a two way communication device with the astral brain. The motivation to believe this model is incredulity that the physical brain can pull off the stunt of self referencing consciousness. They also believe the reports of those who have taken DMT, that the universe has extremely complicated other-levels of reality.
One problem for your argument, is that these other planes that make our brain work, may not be related to God, any more than our physical plane.
It is difficult to disprove this remote control idea, since we do not have logic analysers that can tell us what is currently happening in a human brain. We also don't know if the brain is some kind of elaborate hoax, and it's just a fake jelly thing which is made to look convincing, up until the year 2090, when we find out that it's a hoax.
So, how do we produce counter arguments to these ideas, when we may be being hoaxed?
One thing that stands out, is the correlation with intelligence and brain size. Different humans can be really dumb and really smart. We all have the same brain size, so what's happening here, if our brain is just a remote control? We have pretty good evidence that our intellect can be messed around with, if we damage small bits of brain, or take "upper" drugs. That really shouldn't be possible, if the astral plane is doing all the work. We also have a pretty good hunch that we could breed smarter people, or dumber people, if we put our minds to it. That activity starts to rule out a spiritual reason why some people could be born dumb.
Next we can look at animals with very small brains, that behave intelligently. Birds have nut-sized brains, but behave as if they are conscious, and sometimes very smartly. We can tell from this science bird, that the remote control part of the brain must be very small.https://www.youtube.com/watch?v=p0E1Wny5kCk
If the remote control component is very small, then what's the rest of it for? Backfill?
You might make a case that each species is as dumb or smart as it needs to be. However, we need humans to be smarter, but half of them stubbornly refuse to have an IQ above 100.
Also, you could have the idea that astral brains reincarnate and get smarter each time. So, they start in birds or rats, and eventually learn to be humans. If that's the case, then humans should start out as smart as a rat. However, they seem to start at the bottom of a dribbling learning curve. Human babies would start out, scuttling around the room, and sniffing things. Their parents would say , "Oh yeah. He was a rat in his last life." There doesn't seem to be any development of the astral brain, so consequently it's difficult to explain why some humans would arrive with low intelligence, or high intelligence, and be complete arseholes. You could posit that the astral brain was responsible for low intelligence, but it's more likely we would find some neurotransmitters that are a bit low, and some parts not as big.
The astral brain obviously doesn't have any memories, or it would be able to compensate for Alzheimer's.
It doesn't really jump out at us.