Preheat oven to 350 degrees.
Add 4 tbsp butter to a large dutch oven over medium heat. Gently stir as it begins to melt and toss in 5-6 fresh sage leaves and 2-3 fresh thyme sprigs. Stir and saute herbs for 1-2 minutes. Remove herbs, set on paper towel and reserve until later. Add the 3/4 cup diced onions and 4 minced garlic cloves to melted butter and cook 3-4 minutes or until softened.
Once onions are translucent, add 4 cups butternut squash, 2 tsp dried sage, 1 tsp dried thyme, 1 tsp sea salt and 1/4 tsp black pepper, stir to combine. Add 1 1/2 cups vegetable broth and the reserved herbs (previously cooked in butter), and bring to a boil. Reduce heat to low and simmer 9-10 minutes, stirring occasionally, until the squash is tender.
Remove the herbs and discard. Stir in the milk, then transfer mixture to a high-speed blender and puree until smooth.
Meanwhile, cook pasta according to package direction - bringing water to a boil in a large pot, then adding pasta and cooking 6-7 minutes, leaving them just slightly undercooked, as they’ll continue to cook in the oven. Once pasta is cooked, drain and set aside.
Add the pureed sauce back to the dutch oven on medium heat. Grate 8 oz white cheddar cheese, 4 oz smoked gouda and 4 oz Parmigiano Reggiano, reserving 1/2 cup of the Reggiano. Add shredded cheese a handful at a time, stirring well between each addition to ensure it melts smoothly. Stir in the pasta. Taste and add additional seasoning if desired.
Spray 9x13 glass or ceramic dish with nonstick spray. Add the cheesy butternut squash pasta mixture to the dish, then top with the remaining 1/2 cup Reggiano and lightly stir.
In a small bowl, stir together 1 tbsp melted butter, 1/2 cup almond flour, 1/4 cup chopped sage, 1 tsp fresh thyme, pinch sea salt and pepper, and sprinkle over the top.
Bake for 15 minutes, then broil another 1-2 minutes until the crumb topping is golden brown. Watch closely to make sure it doesn’t burn.
Serve immediately and enjoy!