Preheat the oven to 400 degrees F.
Bring a large pot of water to a boil. Add some salt and then the macaroni. Cook to al dente according to the package directions. Drain and hold until the cheese sauce is ready.
Heat the oil in a medium pot over medium heat. Add the red onions and cook, covered, until soft, a couple of minutes. Add the garlic and bell peppers and cook an additional 2 to 5 minutes, being careful not to burn the garlic. Add the ground beef and sprinkle with salt and pepper; cook until browned, stirring to break up the beef into small pieces. Add the chili powder, cumin, paprika and oregano, and cook until the spices are fragrant. Add the beans and their liquid, the tomatoes and their juices, and the tomato paste; simmer for 5 to 10 minutes.
In a separate saucepot, melt the butter over low heat. Add the flour and cook, whisking, for 1 minute. Whisk in the milk, raise the heat to high, and bring the mixture to a boil; cook, whisking, until thickened. Removing from the heat and whisk in the cream cheese, Cheddar, mustard, Worcestershire and some salt and pepper. Pour the pasta into the cheese sauce and stir to combine.
Mix the chili into the macaroni and cheese. Transfer to a serving bowl and top with additional Cheddar and the green onions. Serve with corn chips.