In a large Dutch oven, melt 2 tablespoons of unsalted butter with 2 tablespoons of olive oil over medium heat. Add sliced yellow onions and cover, cooking for 10 minutes. Uncover and lower the heat to medium-low, stirring occasionally for about 40 minutes, until the onions are deeply caramelized and golden brown.

In the same skillet, melt 2 tablespoons of butter over medium heat. Stir in 1 cup of panko breadcrumbs along with 1 teaspoon of fresh thyme. Toast the breadcrumbs until golden brown and fragrant, about 3-5 minutes. Season with kosher salt and pepper.

Preheat your oven to 425°F (220°C). Lightly grease a baking dish with butter or non-stick spray.

Bring a large pot of salted water to a boil. Add the short pasta and cook just shy of al dente, about 2-3 minutes less than the package directions. Drain the pasta and rinse briefly with cold water.

In the same Dutch oven, melt 4 tablespoons of unsalted butter over medium heat. Whisk in 1/4 cup of all-purpose flour and cook for 2-3 minutes until light golden. Gradually whisk in 2 cups of half and half, bring to a simmer until thickened. Stir in 1 tablespoon of Dijon mustard, nutmeg, and 1/2 cup of heavy cream.

Remove from heat and stir in 1 cup of white cheddar cheese and 1 cup of Gruyère cheese until melted. Fold in the caramelized onions and cooked pasta until well combined. Transfer to the greased baking dish and top with panko breadcrumbs. Bake for 15-20 minutes until golden and bubbly.