Peel and slice the onions nice and thin on a mandolin about a quarter of an inch thick.
Toss the sliced onions together to break up the rings.
Mix together salt, black pepper, smoked paprika, granulated garlic, dry mustard, brown sugar, cayenne, and fresh thyme leaves.
Add a couple of tablespoons of olive oil to the onions and toss to coat.
Sprinkle about half of the spice blend on the onions and toss to combine.
Sprinkle the remaining half of the spice blend on the onions and toss again.
Place the onions in a greased 13 by 9 baking dish in a couple of layers.
Add the first layer of onions.
Add 2 oz of freshly grated Tillamook mild cheddar cheese.
Add 2 oz of freshly grated Gruyère cheese.
Add another layer of onions on top.
Add another 2 oz of Tillamook cheddar cheese.
Add another 2 oz of Gruyère cheese.
Sprinkle about a half cup of freshly grated pecorino romano cheese on top.
Dot the top with 3 Tbsp of butter cut into small pieces.
Cover the baking dish tightly with foil.
Bake in an oven preheated to 350°F for 45 minutes.
Remove the foil.
Bake for another 30 minutes.
