All matter is chemistry of course. But the chemical imbalance theory means the transmitter substance theory. The theory of chemical imbalance causing mental illness is about transmitter substances, for instance serotonin, dopamine, noradrenalin and so on. The THEORY does not include the other matter. If you have an issue with the chemical imbalance theory not including the chemical processes in other systems of the brain, maybe talk to the people behind the theory since I didn't come up with the theory.