Preheat oven to 350°F. Press piecrust into a 9-inch pie plate; crimp edges. Freeze until firm, about 15 minutes. Line piecrust with aluminum foil; fill with pie weights or dried beans. Bake in preheated oven until golden brown, about 20 minutes. Remove foil and pie weights. Return piecrust to oven; bake until bottom is dry, about 5 minutes. Let cool about 10 minutes.

Meanwhile, prepare pasta according to package directions. Drain, rinse, and set aside.

Cook butter and thyme sprigs in a medium saucepan over medium until butter is melted, 3 to 4 minutes. Add flour; cook, stirring constantly, until a light golden paste forms, about 1 minute. Gradually add milk in a steady stream, whisking constantly, until fully combined. Remove and discard thyme sprigs. Add mustard, pepper, and salt to flour mixture; cook, whisking constantly, until smooth and thick, about 2 minutes. Gradually and slowly add cheeses, stirring to melt completely between each addition. Whisk vigorously until mixture is melted and smooth. Remove from heat; gently fold in pasta.

Spoon mixture into prepared piecrust. Return to oven, and bake at 350°F until golden brown, 25 to 30 minutes. Sprinkle with thyme leaves. Let cool 10 minutes; slice into 6 wedges.