Preheat the oven to 350°F. Butter an 8 x 11-inch baking dish and set aside.
In a large pot of boiling salted water, cook the pasta al dente according to package instructions. Drain, rinse and set aside to cool.
In another large saucepan over medium-high heat, melt the butter, then add the flour to make the roux. Whisk the flour and butter until they are combined and golden, about 2 minutes.
Slowly pour the milk, whisking as you pour. Add the Dijon mustard and season with salt and pepper to taste. Bring the mixture to a boil, then reduce to low and simmer, occasionally whisking until sauce is thickened, about 5-7 minutes.
Stir in the cheeses, then fold in the pasta. Transfer to the prepared baking dish and sprinkle with panko breadcrumbs. Bake until the breadcrumbs are golden and the edges are bubbly, about 20-25 minutes.