As has been demonstrated numerous times, autistic brains are built on a non-standard blueprint, including differences in the amygdala, hippocampus, parietal lobes, and cerebrum. In cases of mental illness, the patient's brain is pretty close to standard issue (leaving aside such aberrations as lesions and tumors); the patient merely displays thought patterns, whether due to biochemical maladjustment or maladaptive thinking, that differ significantly from the norm, and cause distress to the patient or others (a psychopath may be perfectly comfortable with his need to ritually kill and eat three human beings every full moon, but it definitely causes his victims distress!).
By the same token neither hydrocephalia, fetal alcohol syndrome, nor Down's syndrome is a mental illness, even though they present quite clearly in brain function, as they are matters of neuroanatomy, not maladaptive thought processes.
_________________
Sodium is a metal that reacts explosively when exposed to water. Chlorine is a gas that'll kill you dead in moments. Together they make my fries taste good.