Heat olive oil in a large skillet over medium heat. Season both sides of the chicken breasts thoroughly with ground black pepper, smoked paprika, garlic powder, onion powder, cayenne pepper, and salt. Cook undisturbed for about 6-7 minutes on each side until golden brown and cooked through. Remove from heat and set aside.
In the same skillet, add honey, apple cider vinegar, soy sauce, and Dijon mustard. Stir while scraping up any browned bits. Bring to a gentle simmer for approximately 5 minutes until it thickens slightly. Return the chicken to the skillet and let it simmer again for another 5 minutes.
Bring a large pot of salted water to boil. Add elbow macaroni and cook until al dente, about 7-8 minutes. Drain and set aside without rinsing.
In another large saucepan, melt butter over medium heat. Whisk in flour to create a roux, cooking for 1-2 minutes. Slowly pour in whole milk while whisking continuously until thickened, about 4-5 minutes.
Once the cheese sauce is smooth, add shredded cheddar and mozzarella, stirring gently to coat the warm macaroni evenly. Serve alongside the sweet and spicy honey-glazed chicken.