In a large, wide, deep skillet or pot, melt 2 tablespoons of butter over medium heat. Add the sliced onions and cover the skillet, cooking for 5 minutes.

After 5 minutes, uncover the skillet, reduce the heat to medium-low, and add ½ teaspoon of salt, ½ teaspoon of pepper, the thyme sprigs, and the bay leaves. Cook while stirring frequently for 40 to 60 minutes, until the onions are deeply caramelized and sweet.

While the onions are cooking, preheat your oven to 425 degrees F and butter a 9 x 13-inch baking dish.

Once the onions are caramelized, remove the thyme sprigs and bay leaves. Increase the heat to medium, add the remaining 2 tablespoons of butter and ½ teaspoon of salt.

Sprinkle the flour over the onions and cook, stirring constantly for 2 minutes.

Gradually add the warmed milk in half-cup increments, stirring often and bringing the mixture to a gentle simmer between additions. Continue adding milk and stirring until the mixture thickens, which should take about 25 minutes.

Meanwhile, cook the pasta according to package instructions, drain it, and transfer it to the prepared baking dish.

Remove the skillet from heat and fold the grated cheese into the roux, reserving ¼ cup of cheese for topping. Pour the cheese mixture over the pasta and gently toss to combine.

In a small bowl, mix the remaining tablespoon of butter with the panko and reserved cheese, using your fingertips to combine. Add a pinch of salt and pepper.

Sprinkle the panko mixture over the top of the mac and cheese. At this point, the dish can be covered and refrigerated for up to 3 days. If refrigerated, let it sit at room temperature for 30 minutes before baking.

Bake the mac and cheese in the preheated oven for about 25 minutes, or until the top is golden and the filling is bubbly. If desired, garnish with additional thyme sprigs or leaves before serving.