Pre-heat oven to 400 degrees.
Place tomatoes on rimmed baking sheets in a single layer. Drizzle tomatoes with about 2 Tbsp of olive oil and sprinkle each with 1 tsp thyme leaves. Season with salt and pepper. Bake until tomatoes are soft, about 20 minutes. Remove from oven and leave oven on.
Place bread in a food processor and process until coarse crumbs form. In a medium skillet over medium heat, melt butter and remaining 1 Tbsp olive oil. Add breadcrumbs and toss to coat. Season with salt and pepper and set aside.
Bring a large pot of salted water to a boil over high heat. Add macaroni and cook for about 5 minutes, until almost al dente. Drain macaroni and run under cold water to stop cooking. Transfer to a large bowl.
In a small bowl, whisk ⅓ cup of the milk and the flour until smooth.
In a medium saucepan over medium heat, melt remaining 1 Tbsp butter. Stir in nutmeg, cayenne, garlic powder, remaining ½ tsp thyme leaves, and 1 tsp salt. Add remaining milk and chicken stock. Whisk in flour mixture and bring to a boil, whisking frequently. Once boiling, reduce to a simmer and cook for about 8 minutes, continuing to whisk frequently. Add cheddar and parmesan and stir until melted. Pour mixture over macaroni and stir until well coated.
Put eight 10 oz ramekins on a baking sheet and place 2 tomato slices in bottom of each. Divide macaroni mixture evenly among ramekins and top each with a tomato slice. Sprinkle with breadcrumbs and thyme sprigs.
Bake until bubbling and golden brown, about 30 minutes. Serve immediately.