Sounds like a confusing situation to be in right now. I was diagnosed the same way with a doctor telling me I needed to eat gluten free even though my blood results were inconclusive, I was bummed and confused by this. I understand how tough it is to tell everyone you have a "gluten allergy" when really you aren't sure exactly what you have going on and would really love to eat that pizza too! My recommendation is to continue eating gluten free for the time being to give your body adequate time to decide what it thinks about the diet but also to look at all possible reasonings for why your thyroid and other non digestive symptoms improved on the diet. Maybe eating gluten free or reintroducing meat expanded your diet and gave you more nutrients or you made a lifestyle change of some kind while gluten free that is helping you. For example if you were vegetarian pre-gluten free then it would have been harder for your body to absorb the nutrients such as iron, zinc, and B12 but once eating meat your body was given those nutrients in a more readily absorbable fashion. Don't settle for your diagnosis until you are comfortable with it and know you are or are becoming a healthy person.