Preheat oven to 350°F. Get the pasta cooking, and start the sauce. Melt 2 tbsp butter, then whisk in flour and heat through. Whisk in the milk and let it heat to a simmer, whisking until it thickens. Add all but 1/4 cup of the cheese and whisk until completely melted.
Melt the remaining butter in a small bowl and stir in the panko.
Add the tomatoes, scallions, and salt and pepper to taste to the cheese sauce. Mix in the pasta, then dump into an 8x8 baking dish. Top with remaining cheese, then sprinkle on panko.