No, an antibody test can't rule out nodules on your thyroid, on the other hand, nodules don't determine autoimmunity; that's done mostly via the antibody tests, but can also, sometimes be done through characteristics of the thyroid gland itself.
It's not true that nodules are rare with Graves Disease since thyroid nodules are common with both autoimmune thyroid conditions - either Graves or Hashimoto's. It's always a good idea to get a scan to check for nodules, but even if you have them as many of us do, most nodules are nothing to worry about.
I'm curious as to how they've determined your hyperthyroidism can't be caused by an active nodule, if you haven't been scanned for nodules. It's possible to have an active nodule AND have an autoimmune condition.
Not all B12 deficiency is autoimmune. It's only autoimmune if it's Pernicious Anemia. The most common causes of B12 deficiency are poor diet or poor absorption.
You asked: "Would I not have tested positive for antibodies anyway because I have MS and B12?"
The antibodies for autoimmune conditions can get confusing. The antibodies for an autoimmune thyroid condition are not the same ones that would be present in MS, nor would the test(s) done to determine MS be the same one(s) done to determine autoimmune B12 deficiency (Pernicious Anemia) or autoimmune thyroid condition. The thyroid antibodies only attack the thyroid, whereas other antibodies attack other parts of the body, depending on the antibodies and the diagnosed disease.
For that matter, there are actually 3 antibody tests to determine autoimmune thyroid condition, so depending on which test they did on you, you could have been misdiagnosed and even though you have hyperthyroidism, you might be in a hyper phase of Hashimoto's and not have Graves Disease at all because some of the antibodies can be present in both Hashimoto's and Graves... confusing...
Which antibody test did they order for you?
It was a very positive TRAb antibody test. They also say it would not alter their treatment plan. This is why they say definitely Graves. I still feel I want the scan and will ask again as I would rather know if there are nodules too.
Answer from the specialist is basically Nodules are pretty rare with Graves and carry a low risk. Therefore no need to have scan just yet.