Preheat oven to 350°F (175°C).

Heat a large skillet over medium-high heat. Once hot, add the olive oil, 2 tablespoons unsalted butter, and diced yellow onions.

Reduce the heat to low, cover the skillet with a lid, and cook for 25-30 minutes, or until the onions are significantly softened.

Remove the lid and increase the heat to medium. Continue to cook, stirring occasionally, until the onions turn golden brown and are deeply caramelized. Season with 1 teaspoon sea salt and 0.5 teaspoon black pepper.

Cover the pan and remove it from the heat. Set aside.

In a separate large saucepan over medium heat, melt 0.5 cup unsalted butter.

Add 0.5 cup all-purpose flour and whisk constantly for 1-2 minutes, or until the mixture turns a light brown color (this is called a roux).

Remove the saucepan from the heat. Gradually pour in the 2 cups warmed whole milk and 1 cup beef stock, whisking constantly to prevent lumps.

Return the pan to medium heat and whisk continuously for another 3-5 minutes, or until the sauce has thickened.

Stir in 2 teaspoons kosher salt, 0.5 teaspoon ground mustard powder, 0.25 teaspoon garlic powder, and 0.25 teaspoon cayenne pepper (if using).

Add 1 cup sharp Gruyere cheese and 0.5 cup mozzarella cheese, along with the caramelized onion mixture. Stir until all the cheese is melted and the sauce is smooth.

Pour the prepared cheese sauce over the cooked and drained 16 ounces elbow macaroni in a large bowl. Stir to combine thoroughly.

Add 2 cups shredded rotisserie chicken to the macaroni and cheese, stirring until completely mixed together.

Transfer the macaroni and cheese mixture to a baking dish. Top evenly with 0.25 cup shredded Gruyere cheese.

Bake, uncovered, in the preheated oven for 12-15 minutes, or until the topping is golden brown and bubbly.

Season with additional salt and black pepper to taste, and garnish with 1 tablespoon chopped fresh thyme before serving.