For the mac and cheese: Preheat the oven to 375 degrees F. Grease a 9-by-13-inch baking dish with nonstick cooking spray and set aside.
Bring a large pot of salted water to a boil and cook the pasta until al dente, about 6 minutes. Drain and set aside.
Meanwhile, heat the cream and sour cream in a medium saucepan over medium-low heat until the mixture begins to steam. Do not boil. Take if off the heat, stir in the Gouda, Havarti, truffle salt, jalapenos, 1 1/2 teaspoons salt, 2 3/4 cups of the Cheddar and 3/4 cup of the mozzarella and continue to stir until the cheese has completely melted. Stir the penne into the cheese mixture until completely coated.
For the cracker topping: In a small bowl, mix the crushed crackers with the melted butter until coated.
Pour the penne mixture into the prepared baking dish and sprinkle with the cracker topping, remaining 1/4 cup Cheddar and remaining 1/4 cup mozzarella. Bake until the sauce is bubbly and the crackers are browned on top, 30 to 35 minutes.