Preheat oven to 450 degrees. In a large pot, combine the milk, cream cheese and Velveeta over medium heat. Stir until cheeses are melted and mixture starts to simmer, then whisk in 2 cups shredded monterey jack cheese and 2 cups shredded cheddar cheese until melted.
Fold the macaroni and marinara sauce into the cheese sauce to combine completely and season to taste with salt and pepper. Spread onto a baking sheet and top with remaining 1 cup shredded monterey jack cheese, 1 cup cheddar cheese, onions, red and green peppers and pepperoni.
In a medium bowl, stir to combine panko, olive oil, Italian seasoning, salt and pepper. Sprinkle over macaroni and cheese, then bake until top is crisp and cheese is melted, about 15-20 minutes.