Heat the butter in a large skillet over medium heat until completely melted. Add the onion, garlic, peppercorn, bay leaf, and thyme and cook until the onions have softened, about 5-7 minutes. Add the tomato paste and cook for another 5 minutes, stirring every couple of minutes. Add two of the diced tomatoes and stir to combine. Bring the heat down to low and allow the mixture to cook for 30 minutes, or until the tomatoes have softened and broken down slightly, stirring every 5-8 minutes. Pour the mixture into a blender and blend at high speed until a smooth puree forms.

Preheat the oven to 375 degrees Fahrenheit. Pour the tomato soup back into the skillet and place back over low heat. Stir in the milk and cream until fully incorporated and the mixture is hot but not boiling. Whisk in the flour until smooth, then stir in the gouda and cheddar and continue stirring until the grated cheese has melted. Now, gently stir in the macaroni and sourdough bread cubes until they are coated with the cheesy tomato soup. Top with the bread crumbs, Parmesan, and black pepper and bake in the oven for 30-45 minutes, or until the macaroni is toasted on top and the bread crumbs are golden brown at the tips. For a crunchier top, lean more towards the 45-minute roasting time (but keep an eye on it, all ovens have their personalities). Remove from oven and allow to cool for 10 minutes before serving.