Cook the pasta: Boil the shells in a large pot of well-salted water according to the package directions. Drain, but don't rinse.
Toast the breadcrumbs: In a small skillet, melt 2 tablespoons of the butter over medium-high heat. Add the panko and cook, stirring constantly, until toasted and golden brown, about 4 minutes. Remove from the heat and set aside.
Make the roux: In a large skillet or Dutch oven, melt the remaining ¼ cup butter over medium-high heat. Whisk in the flour and cook, stirring, until the mixture is light golden, about 2 minutes.
Add the milk: Gradually whisk in the milk, salt, and pepper. Reduce the heat to medium and whisk continually until the mixture bubbles and thickens enough to coat a spoon, 4 to 5 minutes.
Melt in the cheese: Remove the pan from the heat. Gradually whisk in the cheddar, Velveeta, Parmesan, sour cream, ground mustard, garlic powder, and nutmeg, adding the cheese a handful at a time, until melted and smooth. Taste and season with additional salt and pepper if desired.
Toss and serve: Add the cooked pasta and stir to coat. Sprinkle with the toasted breadcrumbs, garnish with fresh herbs, and serve immediately.