Cook pasta in a large pot of salted boiling water according to package directions. Drain.
Meanwhile, in a large Dutch oven or other heavy-bottomed pot, melt butter over medium-high heat. Add flour; cook, stirring until the mixture is golden brown, about 2 minutes.
Gradually whisk in the milk, salt, ground mustard, garlic powder, onion powder, ground nutmeg, and black pepper. Reduce heat to medium; whisk continually until the mixture bubbles and thickens slightly, about 4-5 minutes.
Remove from the heat; gradually whisk in the pumpkin, cheddar, gouda, and Parmesan until the sauce is smooth. Taste and season with additional salt and pepper, if desired.
Add cooked pasta; stir to coat. Garnish with fresh herbs, Parmesan cheese, and crushed red pepper flakes, if desired.