Begin by peeling and thinly slicing the sweet onions using a mandolin, aiming for slices about a quarter of an inch thick. Toss the sliced onions to separate the rings.
Prepare the spice blend by combining the salt, black pepper, smoked paprika, granulated garlic, dried mustard, brown sugar, cayenne, and fresh thyme leaves in a bowl.
Sprinkle half of the spice mixture over the onions and toss to ensure they are well coated. Then add the remaining spice blend and toss again.
Drizzle a couple of tablespoons of high-quality olive oil over the onions and mix to coat evenly.
Grease a 13 by 9-inch baking dish and layer the onions, starting with a generous layer at the bottom.
On top of the first layer of onions, add 2 ounces of freshly grated Tillamook mild cheddar cheese.
Next, sprinkle 2 ounces of Gruyere cheese over the cheddar.
Add another layer of onions on top of the cheeses, followed by another 2 ounces of Tillamook cheddar cheese.
Top this layer with the remaining 2 ounces of Gruyere cheese.
Finish by sprinkling about half a cup of freshly grated Pecorino Romano cheese over the top.
Dot the mixture with small pieces of butter, totaling 3 tablespoons.
Cover the dish tightly with foil and bake in a preheated oven at 350°F for 45 minutes.
After 45 minutes, remove the foil and continue baking for an additional 30 minutes, or until the dish is fully cooked.
