Preheat oven to 375 degrees F (190 degrees C) and place a 9×13 baking dish on a baking sheet, or arrange 6-8 individual ramekins on a baking sheet. Set aside.
Bring a large pot of cold water to a boil. Season with Salt (to taste) and add the Penne Pasta (1 pound). Stir often and cook 2 minutes under suggested cooking time (it will finish in the oven). It should not be overly soft. Drain and set aside.
To make the pumpkin cheese sauce, heat a large pot over medium heat. Add Butter (3 tablespoon) and melt. Add the All-Purpose Flour (3 tablespoon) and whisk together. Cook for a few minutes until the mixture smells nutty.
Stream in the Whole Milk (4 cup) while whisking the entire time. Bring to a simmer and allow the milk to thicken. You will know the sauce is ready when the back of a wooden spoon is coated and you can leave a line with your finger.
Once thickened, season with the Dijon Mustard (1 tablespoon), Salt (1 teaspoon), Freshly Ground Black Pepper (1 teaspoon), Dried Thyme (1/2 teaspoon), Onion Powder (1/2 teaspoon), Garlic Powder (1/2 teaspoon), and Paprika (1/2 teaspoon).
Stir in the 100% Pumpkin Purée (3/4 cup).
Turn off the heat and add the Cheddar Cheese (2 cup) (reserve a bit for the topping), Parmesan Cheese (1/2 cup) (reserve a bit for the topping), and Fontina Cheese (1/4 cup). Stir until the cheeses melt and the sauce is evenly incorporated together.
Add the cooked penne pasta and stir to combine. Pour into the baking dish or portion out into the individual ramekins. Top with reserved cheddar cheese and parmesan cheese.
To make the sage breadcrumb toppings, heat a small pot over low heat. Add Butter (2 tablespoon) melt. Add the Fresh Sage (2 tablespoon) and cook until crispy, about a minute. Remove from heat and allow to slightly cool.
In a small bowl, combine the Panko Breadcrumbs (1/4 cup) and plain Breadcrumbs (1/4 cup). Add the crispy fresh sage and butter. Stir with a spoon and sprinkle evenly over the mac and cheese.
Bake in the center rack for about 25-30 minutes, until golden brown and bubbly. Serve right away.