Preheat oven to 350 degrees F. In a skillet melt 3 tablespoons of butter. Add shallot and cook, stirring occasionally for 3 minutes, or until softened. Add the mushrooms, salt and pepper, thyme, and rosemary. Cook, stirring occasionally for 2 minutes more or until the mushrooms are lightly golden. Transfer mixture to a bowl and stir in chives or parsley and set aside. Now make the sauce. In a saucepan set over moderately low heat melt butter, add the flour and cook the mixture, whisking, for 3 minutes. Add milk, bring mixture to a simmer, whisking, and simmer, stirring occasionally for 5 minutes or until lightly thickened. Remove saucepan from the heat and stir in the fontina, mozzarella, and gorgonzola and 2/3 cup of the Parmesan cheese, a little at a time, until well combined. Season to taste with salt and pepper. To assemble the gratin; in a large bowl toss the pasta with the mushroom mixture. Add 3/4 of the sauce and stir gently to combine. Using remaining 3 tablespoons of butter, butter a 2 to 3 quart gratin dish arrange pasta and diagonal rows of the tomatoes. Top evenly with remaining sauce. Place in oven and bake for 25 minutes or until bubbling and golden.