Preheat oven to 375°F (190°C). Lightly grease a 9x13-inch baking dish or oven-safe cast iron skillet.

Bring a large pot of salted water to a rolling boil. Cook pasta 1-2 minutes shy of al dente according to package directions (it will continue cooking in the oven). Drain and set aside.

In a large saucepan, melt 2 tablespoons butter over medium heat. Whisk in flour and cook for 1-2 minutes until bubbling and lightly golden. Whisk in minced garlic and cook for 30 seconds.

Gradually pour in warmed whole milk and broth while whisking continuously to prevent lumps. Simmer gently for 3-4 minutes until the sauce coats the back of a spoon.

Whisk in butternut squash puree, smoked paprika, ground nutmeg, Dijon mustard, 1/2 tsp salt, and 1/4 tsp black pepper until smooth and velvety.

Remove sauce from heat. Gradually fold in 2 cups of the sharp cheddar and all 1.5 cups of fontina cheese until completely melted and silky smooth.

Add drained pasta to the cheese sauce, tossing thoroughly until every curl is generously coated. Transfer into the prepared baking dish and sprinkle the remaining 1/2 cup cheddar over top.

In a small bowl, melt remaining 1 tbsp butter and toss with panko breadcrumbs and minced fresh thyme. Scatter evenly over the mac and cheese.

Bake uncovered for 20-25 minutes until bubbling around the edges and the panko topping is deeply golden-brown and crispy. Let rest 5 minutes before serving.