Prepare the Butternut Squash: Peel, seed, and dice the butternut squash into cubes, boil until tender (about 15 minutes), then mash until smooth and set aside.
Cook the Pasta: In a large pot of salted boiling water, cook the mezzi rigatoni according to package instructions until al dente. Drain and reserve about half a cup of pasta water.
Make the Cheese Sauce: In a saucepan over medium heat, melt the unsalted butter, whisk in the flour until smooth to create a roux, then gradually add in the milk while whisking continuously until thickened.
Combine Cheeses & Seasoning: Once the sauce has thickened, remove from heat and stir in cheddar cheese, smoked gouda, parmesan cheese, salt, nutmeg, pepper, and Tabasco sauce until fully melted.
Mix Everything Together: Stir in the mashed butternut squash and cooked pasta into the cheese sauce mixture until well combined.
Bake (Optional): Transfer everything into a greased baking dish and bake at 350°F (175°C) for about 20 minutes until bubbly and golden on top.