Preheat oven to 400 degrees, Cook pasta until ‘al dente’, or firm, about 2 minutes less as directed on package, drain water from pasta reserving until needed. It is important not to fully cook pasta, as it will continue to cook in the oven.
In a large pan, add 4 tablespoons of butter, shallots and red bell pepper over medium high heat. Cook until softened and shallots turn light brown, about 4-5 minutes.
Whisk in flour, stirring until bubbly and fragrant, about 2-3 minutes. Whisk in milk, stirring until thickened.
Stir in cream cheese, whisking until cheese has melted into the sauce.
Add cheddar cheese, stirring until melted. Add chipotles, green chilies, 1 cup of bacon pieces, and the onion powder. Season sauce with salt as needed.
Add pasta to cheese sauce, tossing until pasta is well coated. Pour into a large casserole dish or into individual ramekins.
In a frying pan, melt the remaining 8 tablespoons of butter. Once melted, stir in Panko until butter is absorbed. Remove from heat and add the remaining cup of bacon and the parmesan cheese to create the Bacon Crumble.
Sprinkle Bacon Crumble over the top of Mac and Cheese. Place into oven and bake for 20 minutes, or until topping is browned and macaroni is bubbly.
In a small bowl, combine diced tomatoes and cilantro, season with salt if desired.
To serve, place macaroni in a bowl, and top with the tomato mixture.