Preheat oven to 400 degrees F. Grease a 9x13-inch baking dish with cooking spray and set aside.
Place the cubed butternut squash on a large baking sheet. Drizzle with olive and toss well. Season with salt and pepper, to taste. Roast for 20 to 25 minutes or until squash is tender. Remove from the oven. Reduce the oven temperature to 375 degrees F.
While the squash is roasting, in a large pot of boiling salted water, cook the pasta to al dente, according to package instructions. Reserve 1/2 cup of the pasta water and then drain well. You can drizzle with a little olive oil and toss so the pasta doesn’t stick while you make the sauce.
Place the roasted butternut squash, ricotta, and reserved pasta water in the blender. Blend until smooth. Season with salt and pepper, to taste.
Use the same large pot you cooked the pasta in to make the sauce. Heat the butter over medium heat. Add the shallot, spinach, sage, and thyme. Cook until spinach is wilted. Add the garlic and cook for 1 minutes. Turn off the heat.
Pour the butternut squash mixture into the pot. Stir in the heavy cream. Add a little pinch of nutmeg, if desired, and the crushed red pepper flakes. Add the pasta to the pot and gently stir until coated. Stir in 3/4 cup of mozzarella cheese and the white cheddar cheese. Season with salt and pepper, to taste.
Pour the pasta into the prepared baking dish. Spread evenly with a spatula. Top with remaining mozzarella cheese, Parmesan cheese, and Panko.
Bake for 20 minutes or until cheese is melty and bubbly. Turn the oven to broil and broil just for a minute or two so the cheese can brown a little. Remove from the oven and let sit for about 5 minutes. Serve and enjoy!