Cook pasta al dente according to package directions in generously salted water. Remove 1 cup pasta water before draining. Melt butter in olive oil over medium-low heat in a large skillet. Increase heat to medium and add onions and HALF of the tomatoes and sauté for 5 minutes. Add garlic and cook an additional 30 seconds. Sprinkle in flour and cook while stirring for 2 minutes (it will be thick). Turn heat to low then slowly whisk in chicken broth, then milk, stirring constantly until smooth. Turn heat to medium high and bring the sauce to a simmer. Stir in spices and continue to simmer until slightly thickened, stirring occasionally. Reduce heat to low and stir in Parmesan cheese until melted, followed by mozzarella cheese until melted, followed by cream cheese until melted. Stir in remaining tomatoes and fresh basil. Stir in pasta until well coated, adding additional reserved pasta water a little at a time if needed to reach desired consistency. Taste and season with additional salt, pepper and/or red pepper flakes to taste. Garnish with freshly grated Parmesan Cheese and additional basil if desired.