Bring a large pot of water to a boil. Add 2 tablespoons salt and cook penne according to package directions until al dente. Reserve 2 cups pasta water before draining.
Meanwhile, heat a large, deep skillet over medium-high heat. Add 2 tablespoons butter and brown the ground beef, seasoning with salt and pepper, until no pink remains (7-8 minutes).
Reduce heat to medium, add diced onions and cook until translucent (3-4 minutes).
Add minced garlic, Italian herbs, and red pepper flakes. Cook for 60-90 seconds until fragrant.
Push meat mixture to one side, add remaining 6 tablespoons butter to empty space. Once melted, sprinkle flour over butter and whisk to create a roux. Cook for 2 minutes.
Gradually whisk in milk until smooth. Add mustard powder and nutmeg, then simmer 3-5 minutes until thickened.
Remove from heat and add cheese in three batches, stirring until fully melted before adding more.
Combine drained pasta with cheese sauce, adding reserved pasta water if needed to adjust consistency.
Simmer on low for 2-3 minutes to meld flavors. Adjust seasoning as needed.
Garnish with fresh herbs and additional Parmesan before serving.