what an interesting question!
I experience different fatigues, amongst them hormonal fatigue. When it's thyroid I'm sluggish, don't want to move my body and I'm cold (a coldness from within, from the bones).
When it's cortisol or progesteron deficiency I get a nervous kind of fatigue. Where I feel threatened but do not have the resources to deal with any stress that might come my way. This fatigue is fixed with hormonal replenishment. Fixing these two fixes thyroid fatigue in turn, together with a daily Kelp/Iodine supplement.
Then there's bodily fatigue. In me it's caused by low blood pressure (and subsequent inability of the nervous system to maintain homeostasis) and digestion. Digestion takes a mighty lot of energy! I've resorted to easily digested superfoods (egg yoke, gelatine) and this preserves my energy. I avoid all vegetables and raw foods.
For the homeostasis fatigue I know no other remedy than resting, reclining and pacing. Always the pacing.
Yes, I'll mention the cell processes fatigue. That'll be the ATP thing you mention, I guess. In my case I think my cells do not get all the amino acids and minerals they need to function properly. They also have some faulty enzymes which hinders the use of the building blocks they do get.
I make sure my cells get everything they need, I pamper them as if they lived in petri dishes. For this I take an amino acid supplement called Biotics Gland thingy. And lots of minerals. And rest (this aids the low blood pressure to deliver the stuffs to the cells).
Some tweaking occurs to aid my specific enzyme mutations. For example: I take extra vitD because I lack some receptors. I am verrry prudent with mB12 because it spurns the processes into overdrive. MAO A mutation asks I do not eat cheese, vanillin or MAO-inhibitors.
Also cell waste disposal, my cells need some help with this. Waste building up fatigues the system severely. I stretch and yawn, aiding the lymph system.
Then there's the fatigue caused by organs. My liver seems to have a hard time with things. It flops out of commission whenever I experience stress. I aid it with the aforementioned Biotics supplement. And by taking HCL with every meal. And by laying down when my food passes the duodenum. And by not eating things that upset my liver (empty calories, alcohol, BBQ)
So to me the fatigue comes from different levels that intercept and influence each other. I can now identify some of them.
There's also the Central Nervous System. Mine gets overworked all the time. I'm "a stress-chicken", that's a Dutch expression. Always alert, always running around, always assuming worst case scenarios. This is very taxing to the body and needs daily doses of zen to neutralize effects. If I don't crippling fatigue will set in.
Whenever the CNS is legitimately stressed out (caused by a life event) I'll need 3 months (or 13 months) to recuperate. This is a normal reaction to stress (see dr. Selye) only in our era we are not used to taking so much time licking our wounds. I try to see this type of fatigue not as part of the illness but as a natural occurence. It does add to the other types I mention above though.
To answer your specific questions, in my opinion and I'm no expert:
1. Say your fatigue is hormonal or due to some medical condition does this mean you can cure it by increasing ATP levels???
nope. Not for the hormonal part anyway. Fatigue from hormones means you lack the effects of those hormones. ATP won't fix that, you need the hormones themselves. Hormones are not scary, you just have to act responsible. Just like when driving a motor bike or feeding a shark/a baby.
2. Does all fatigue have the same mechanism or final underlying cause such as ATP or are there different mechanisms??
I don't know.
I myself look at this problem through the different scales it addresses (whole body, the two vessel structures (blood; lymph), organs, intercellular fluids, cells, cell membranes, enzymes, DNA). Your opinion should probably differ from mine.
3. What are these mechanisms exactly???
I have studied the various levels I mention above because that's my working theory for fatigue. I have not healed however. My energy level has improved from a 15% to 50%. Not tasking the digestion system has been the major contributor to that one.
HRT and full amino acids and minerals have mainly improved mood and have reduced bodily stress levels.
4. Where can I do more reading about this???
hormones: "What your dr. didn't tell you about perimenopause" by dr. Lee; some book by dr. Thiery Hertoghe; website Stop the Thyroid Madness; website of a woman who has addison's and runs marathons. I do not have links for you.... sorry. Do you want them?
cortisol: the wikipedia page.
stress and the havoc it wrecks on the body: work by dr. Selye
sleep: some India dr. who does research on sleep phases. I've got his website somewhere...
cells and membranes: a book for students: "The Cell, a molucular approach"
the body and digestive system: basic biology books and websites. Aimed at students. It's a fascination subject!
As far as I know there is not a coherent field where scientists think about fatigue. You've got to cobble together your own theory, based on your experiences with your own body.
Hospitals where scientist specialize in fatigue, such as Radboud in Nijmegen or some CFS centre, they usually think it's all in the head and the patient just has a poor attitude. They often promote gradual increasing exercise. Run/wheel away from those places.
PS. I think there're other forms of fatigue I have not identified yet. One might very well be The ME Fatigue, the one, the special one.