Bring a large pot of salted water to a boil over high heat. Add the pasta and cook until al dente according to package instructions. Drain.
Meanwhile, preheat the oven to 375°F degrees with a rack in the center position. Spray a 9x13-inch baking dish with cooking spray.
Add ½ cup of the butter to a large saucepan over medium heat. Cook, stirring occasionally until melted. Sprinkle the flour over the butter and cook, whisking constantly until flour is fully absorbed and a thick paste is formed, 1 minute.
Slowly whisk in the milk one cup at a time. Cook, stirring occasionally until the sauce has thickened, 5 minutes. Stir in the salt, garlic powder, pepper and cream cheese. Cook, stirring, until the cream cheese is fully incorporated. Stir in 2½ cheddar cheese and 3½ cups pepper jack cheese, until melted.
Reserve ¼ cup of the bacon for garnishing. Stir the remaining bacon and chopped jalapeños into the cheese sauce. Add the cooked noodles to the prepared baking dish. Pour the cheese sauce over the noodles and stir until fully incorporated.
Add the remaining ½ cup of butter to a small skillet set over medium heat. Once melted, remove from heat and stir in the panko breadcrumbs, until fully coated.
Sprinkle the macaroni and cheese evenly with the remaining ½ cup cheddar cheese and ½ cup monterey jack. Top evenly with the sliced jalapeno. Sprinkle evenly with the panko breadcrumbs.
Bake until panko is golden brown, the cheese is melted and the sauce is bubbling, 30-40 minutes.