How to Make It
Preheat oven to 425°F. Toss tomato slices with 1 tablespoon of the oil, and place tomatoes in a single layer on a wire rack set in rimmed baking sheet lined with aluminum foil. Sprinkle evenly with 1/2 teaspoon of the salt and 1/4 teaspoon of the pepper. Bake in preheated oven 10 minutes, and set aside. Reduce oven temperature to 375°F.
Cook pasta according to package directions, reserving 3/4 cup cooking water before draining; keep warm.
Melt butter in a saucepan over medium. Whisk in flour, and cook, whisking constantly, 2 minutes. Graduallly whisk in milk, and bring mixture to a simmer. Cook, stirring occasionally, until thickened, about 5 minutes; sprinkle with nutmeg, and remaining 1/2 teaspoon salt and 1/4 teaspoon pepper. Whisk in provolone cheese until smooth, and stir in vinegar. Pour cheese sauce over pasta, and stir to combine. Thin mixture as needed with reserved cooking water.
Pour half of pasta mixture into a lightly greased 3-quart baking dish. Top with half of the tomatoes, half of the sliced mozzarella, and chopped basil. Add remaining pasta mixture, and top evenly with remaining tomatoes and mozzarella.
Stir together panko, Parmesan cheese, and remaining 1 tablespoon oil in a small bowl; sprinkle mixture over caprese pasta. Bake in 375°F oven until bubbly, about 25 minutes. Adjust oven to broil, and broil to brown the top, about 2 minutes. Garnish with basil leaves.