Also just because you don't feel ill right after eating a gluten item doesn't mean you are not reacting. Celiac reactions can be delayed so it sounds like your doctor is thinking more allergy with his 'muffin test'.
If you really doubt the first doctors diagnosis then go back on gluten for a couple of months at least and then get retested. That is if your body hasn't given you the answer after a couple weeks.
I agree. I don't react immediately every single time I was glutened, but the severity of my symptoms do grow with time (repeated glutening).
From what I know of biopsies (and I'm not the most knowledgable) you have autoimmune cells moving into your villi. I think it would be rated as a Marsh I or II. Most doctors won't diagnose celiac disease until a patient hits Marsh III. So basically you have early damage but he won't diagnose you until you are more damaged... it's a broken system.
You also have a positive test (AGA) that shows gliadin sensitivity... Gluten sensitivity and the beginnings of villi damage... all I can say is that I'm glad you plan on staying gluten-free in spite of what the doctor says. LOL