Bring a large pot of water and 1 tablespoon of salt to a boil. Cook the pasta until al dente, about 8-10 minutes or follow package directions. Drain and rinse the pasta and set to the side.
Melt the butter over medium heat in the same pot you cooked the pasta. Add the sage, thyme, and minced garlic and cook until fragrant, about 1-2 minutes. Sprinkle in the flour and whisk together until fully incorporated.
Pour in the milk, add the cheeses, and fold together until the cheese is fully melted. Add the pumpkin puree, dijon mustard, nutmeg, cinnamon, salt, and pepper, and stir until melted and creamy.
Add the cooked pasta to the sauce mixture and mix. If the sauce is too thick for your liking, thin it out using ¼ cup of milk at a time.
Optional: Transfer the pumpkin mac and cheese to a baking dish, top with parmesan cheese and panko breadcrumbs, and bake in the oven at 375°F (190°C) for 10-12 minutes.