Preheat the oven to 350 degrees F (180 degrees C). Grease a 2-quart baking dish.
Bring a large pot of water to a boil and cook noodles for 1 or 2 minutes less than the package recommends for al dente. Drain, rinse with cold water, drain again, and set aside.
Heat olive oil and butter in a large nonstick skillet over medium heat. When butter stops sizzling, add shallots and cook, stirring, until softened, about 2 minutes.
Add garlic, red pepper flakes, and thyme and cook just until garlic is fragrant, 30 seconds to 1 minute.
Stir in flour and cook, stirring, until flour bubbles, about 2 minutes.
Add chicken broth, milk, cream, chicken bouillon granules, and tomatoes. Season to taste with salt and pepper. Cook, stirring, until thickened, 4 to 5 minutes.
Add cooked chicken, noodles, and ½ cup grated Parmesan cheese. Stir well, and pour into prepared pan.
Combine remaining Parmesan cheese with panko breadcrumbs and sprinkle evenly over the casserole.
Bake in the center of the preheated oven until bubbly and lightly browned, about 30 minutes.
Allow casserole to cool for 5 to 10 minutes, garnish with fresh basil, and serve warm.