Your description sounds a lot like what I have going on except my prolactin and cortisol were not tested. I have Hashimotos hypothyroid amid a lot of other syndromes incl fibromyalgia, IBS, RLS, GERD, etc.
I recently had an MRI because of my Neuropathy. It showed empty Sella. I was told empty Sella is of no consequence.
My blood labs showed a high calcium level. Apparently this can denote hyperparathyroidism. A (usually) non cancerous growth on one or more parathyroid (4) organ. I have most of the symptoms including a lot of hair loss over a number of years. It also includes shortness of breath, neausea, palpitations, GERD (or acid reflux), osteoporosis,etc.
BUT my doctor has decided I have FHH which is a congenital form of hyperparathyroid. She is ignoring my other symptoms. I read info from a Parathyroidism group that said FHH is so rare one in several thousand will actually have FHH and I should see another doctor. They even started photographing the tumor for the patient to show their doctor because the form with the tumor is life shortening. Causing several problems i.e. Heart attacks or strokes. So I guess I will be going to another doctor soon.

Can empty Sella have anything to do with a pituitary problem? I know they are not next to each other but I also have MTHFR. And I cannot have food w soy or canola. They give me horrible headaches depending on how much I have eaten (which I now avoid). I mistakenly ate two meals w the oils one day and was blinded by the headaches for 4 days and had cognitive problems for several days after that. It Also causes a tender spot on the right side of my head above my right ear.
It took a lot of my own research and a day without the headaches to figure out what I did or didn't do to not get the headache that day. Doctors kept telling me nothing was wrong.
Also a flattened pituitary gland must be affected in some way. You would think. The first person to leave a message here said something about eyesight which my research did not find. Is this something else I should be aware of?