Bring a large pot of salted water to a boil and cook the pasta according to package instructions until al dente; drain and set aside.
In a small bowl, whisk together the chili powder, chipotle powder, cumin, oregano, kosher salt, coriander, and cayenne until evenly combined.
Heat a large skillet over medium heat and cook the ground beef, breaking it into small pieces, until mostly cooked through, about 5 minutes.
Sprinkle the spice mixture over the beef and stir to coat; if the beef seems dry, add a splash of water. Cook until beef is fully cooked through, then transfer to a bowl with a slotted spoon and set aside.
Return the skillet to medium heat. In a small bowl, mix the flour with 2 tablespoons of the milk to form a smooth paste, then add it to the skillet along with the remaining milk and the sodium citrate, whisking until combined.
Cook the milk mixture over medium heat, whisking occasionally, until it comes to a simmer.
Turn off the heat when simmering and add the shredded cheese a handful at a time, whisking until each addition is fully melted before adding more; return to low heat briefly if needed to finish melting.
Add the cooked, drained pasta to the cheese sauce and stir until evenly coated, then fold in the seasoned ground beef.
Serve immediately on a bed of or topped with shredded iceberg lettuce and garnish with quartered cherry tomatoes.