In a Dutch oven, heat 2 tablespoons of unsalted butter and 1 tablespoon of olive oil over medium heat until shimmering. Add 4 thinly sliced yellow onions, cover, and cook for about 10 minutes until softened. Remove the lid, lower the heat, sprinkle in 1 tablespoon of fresh thyme leaves, and stir occasionally for 40 minutes until the onions are deeply caramelized and golden brown. Set them aside.

In a skillet over medium heat, melt the remaining 3 tablespoons of unsalted butter. Once melted, add 1 tablespoon of chopped thyme leaves and ⅔ cup of panko crumbs, stirring frequently. Cook until the breadcrumbs are golden brown and crispy, about 3-5 minutes. Season them with salt and pepper, then set aside to cool while you prepare the rest of the dish.

Preheat your oven to 425°F (220°C) while you gather your ingredients. Grease a large baking dish with butter or cooking spray to prevent sticking when it's time to serve.

Bring a large pot of salted water to a boil. Add 16 ounces of your chosen short pasta—such as shells or cavatappi—and cook for 2-3 minutes less than the package instructions for al dente. Once cooked, drain the pasta and cool it under cold running water to halt the cooking process.

In the same Dutch oven used for the onions, melt the remaining 3 tablespoons of unsalted butter over medium heat. Whisk in 3 tablespoons of all-purpose flour, cooking for 2-3 minutes to eliminate the raw taste. Gradually whisk in 3 ½ cups of half and half, allowing the mixture to thicken. Stir in 2 teaspoons of Dijon mustard, ¼ teaspoon of freshly grated nutmeg, and ½ cup of heavy cream for extra richness. Finally, fold in 6 ounces of shredded white cheddar and 8 ounces of shredded Gruyere until the cheese is fully melted and the sauce is smooth.

Mix the caramelized onions with the cooked pasta in the béchamel sauce, ensuring everything is perfectly coated. Transfer the mixture to the prepared baking dish, spreading it evenly. Top it with the crispy breadcrumb mixture, then bake for 15-20 minutes or until the top is golden brown and bubbling. Let the French Onion Mac and Cheese rest for 5 minutes before serving.