In a medium bowl, whisk together honey, soy sauce, apple cider vinegar, Dijon mustard, garlic powder, black pepper, and red pepper flakes (if using).

Add the chicken pieces to the marinade and toss to coat. Let it marinate for at least 10 minutes at room temperature, or up to 30 minutes in the refrigerator.

Heat a large skillet over medium-high heat. Add the marinated chicken and cook for 5-7 minutes, or until browned and cooked through. Pour any remaining marinade over the chicken in the last minute of cooking to create a glaze.

Remove chicken from skillet and set aside.

Cook elbow macaroni according to package directions until al dente. Drain and set aside.

In the same skillet (or a clean saucepan), melt butter over medium heat. Whisk in flour and cook for 1 minute, stirring constantly, to make a roux.

Gradually whisk in milk until smooth. Bring to a simmer, stirring frequently, until the sauce thickens. This should take about 5-7 minutes.

Remove from heat and stir in shredded cheddar cheese and Gruyere cheese until melted and smooth.

Stir in salt and nutmeg (if using).

Add the cooked macaroni to the cheese sauce and stir to combine.

Add the cooked honey pepper chicken to the mac and cheese and gently stir to combine.

Serve immediately.