Whether your friend is correct or not has no bearing on the actual existence of God.
He is probably anticipating an argument from you along the lines of, “people in different parts of the world have been worshipping God without knowledge of each other’s existence since the dawn of time, providing objective proof of His existence.”
He would be able to counter with his cerebral God factory argument. However, I doubt any Chrisitian would make this initial argument, as it is a poor one.
Frankly, I think that your friend misconstrued what he had read about the cerebral preception of God. If God were manufactured by our sub-conscious, then we would all be delusional!
It is known that there are parts of the brain that aid in spirituality, and even produce religious ecstacy at times, but to call this the fabrication of God is a bit of a stretch.