Preheat Oven and Prepare Baking Dish: Preheat your oven to 375°F (190°C). Grease a 9×13-inch baking dish or a similar 3-quart casserole dish with butter or cooking spray.

Cook the Pasta: Bring a large pot of heavily salted water to a rolling boil. Add the pasta and cook according to package directions until it is al dente (still has a firm bite). It’s very important not to overcook the pasta at this stage, as it will continue to cook in the oven. Drain the pasta well and set it aside.

Prepare the Panko Topping: While the pasta is cooking, prepare the topping. In a small bowl, combine the panko breadcrumbs, melted butter, fresh thyme leaves, and optional Parmesan cheese. Use your fingers to toss everything together until the breadcrumbs are evenly moistened. Set aside.

Start the Sauce (Sauté Aromatics): In a large Dutch oven or heavy-bottomed pot, melt the 4 tablespoons of butter over medium heat. Add the finely minced shallot and cook, stirring occasionally, for 3-4 minutes until it has softened and become translucent. Add the minced garlic and cook for another minute until fragrant, being careful not to let it burn.

Make the Roux: Sprinkle the flour over the melted butter and shallots. Cook, whisking constantly, for 1-2 minutes. This step cooks out the raw flour taste and is essential for thickening the sauce. The mixture should be bubbly and look like a thick paste.

Create the Béchamel: While continuously whisking, slowly pour in the warmed milk in a thin stream. It’s crucial to add the milk slowly at first to prevent lumps. Once all the milk is incorporated, continue to cook, whisking frequently, for 5-8 minutes, until the sauce has thickened enough to coat the back of a spoon.

Melt the Cheeses: Reduce the heat to low. Add the freshly grated Gruyère cheese to the sauce in handfuls, whisking until each addition is completely melted and smooth before adding the next. Once all the Gruyère is incorporated, remove the pot from the heat completely.

Add the Goat Cheese and Season: Add the room temperature, crumbled goat cheese to the sauce. Whisk gently until the goat cheese has melted and the sauce is smooth and creamy. Whisk in the Dijon mustard, freshly grated nutmeg, and white pepper. Taste the sauce and season with salt as needed. The amount of salt will depend on the saltiness of your cheeses.

Combine and Bake: Pour the drained, cooked pasta into the pot with the cheese sauce. Stir gently until every piece of pasta is thoroughly coated. Pour the mac and cheese mixture into your prepared baking dish and spread it into an even layer.

Top and Bake: Sprinkle the prepared panko topping evenly over the surface of the mac and cheese. Place the dish in the preheated oven and bake for 20-25 minutes, or until the sauce is hot and bubbly and the topping is golden brown and crispy.

Rest and Serve: Let the mac and cheese rest for 5-10 minutes before serving. This allows the sauce to set up slightly. Garnish with additional fresh thyme, if desired, and serve hot.