"but what if the reason that cortisol levels seem to be up and down throughout the day is because as the doctor in the article says, the adrenals are just doing what they are told and since the body is going through an emergency fight-or-flight response, raising cortisol is a natural part of that response, but the brain knows that producing higher cortisol levels is damaging longterm to the body, so maybe the brain knows not to keep cortisol levels continuously elevated?"
There is a negative feedback loop that relays information to the pituitary gland and the hypothalamus via glucocorticoids; the amounts of glucocorticoids present "inform" the pituitary and the hypothalamus to either produce more or less CRH or ACTH, respectively.