Preheat oven to 400°F Spread tomatoes in a single layer on 2 rimmed baking sheets. Drizzle each sheet with 1 Tbsp oil; sprinkle each with 1/2 teaspoons thyme, and season with salt and pepper. Bake until tomatoes have softened, about 20 minutes. (Leave oven on).
Process bread in a food processor until coarse crumbs form. Melt 1 tablespoons butter with remaining tablespoon oil in a medium skillet over medium heat. Add breadcrumbs, and toss to coat, Season with salt and pepper; set aside.
Bring a large pot of water to a boil over high heat. Add 1 Tablespoon salt and the pasta. Cook pasta until almost al dente, about 5 minutes. Drain and run under cold water to stop cooking. Transfer to a large bowl; set aside.
Whisk 1/2 cup stock into the flour in a medium bowl; set aside. Melt remaining tablespoon butter in a medium saucepan over medium heat. Stir in nutmeg, cayenne, remaining 1/2 tsp, thyme, and 1 teaspoons salt. Add milk and remaining 1 1/2 cups stock. Whisk in flour mixture. Bring to a boil, whisking frequently. Reduce to a simmer. Cook 8 minutes, whisking frequently. Add cheeses; cool, stirring until melted. Pour over macaaroni, stirring to combine.
Put eight 4 1/2 x 1 1/4 inch ramekins on a baking sheet, Put 2 tomato slices in bottom of each ramekin, Divide macaroni mixture evenly among ramekins. Top each with a tomato slice. Sprinkle with breadcrumbs and thyme sprigs. Bake until bubbling and golden brown, about 30 minutes.