What you have said doesn’t discredit the concept of adrenal fatigue. Sure high cortisol levels means the person is stressed over time and that their adrenal gland has to be working properly to produce those higher levels of cortisol. And that is not the simple flight or flight response that you cited but ongoing underhanded threats by misuse of relationship.
What you don’t take into account is firstly that any gland or organ in the body that is overworked will suffer fatigue. And secondly “higher levels” doesn’t say a lot. Are those levels as high as they would be in the fight or flight response you cited in a person who is stressed over time as one who is not? In other words the glands may be producing high levels but that is only qualitative judgement. Quantitatively is what counts when you talk about fatigue. You can still be producing higher levels but are those higher levels as high as they would normally?