Cook bacon in a skillet over medium heat until crisp, 6 to 8 minutes; drain, crumble, and set aside.

Boil macaroni in salted water until just shy of al dente, about 1 minute less than package instructions; drain.

In the same pot, melt 2 tbsp butter, whisk in flour, and cook 1 minute. Slowly whisk in milk and cream, simmer until thickened, 3 to 5 minutes. Reduce heat to low, stir in cream cheese, then add cheddar, Monterey Jack, garlic powder, mustard powder, paprika, salt, and pepper; stir until smooth.

Preheat oven to 375°F (190°C). Fold pasta and bacon into sauce, transfer to a greased 2-quart dish. Toss remaining 1 tbsp melted butter with panko and a pinch of salt, then scatter over the top.

Bake 20 to 25 minutes until bubbly and golden. Rest 5 minutes, then spoon into bowls and finish with chives.