Preheat oven to 350°F. Prepare two muffin pans with vegetable pan spray.
In large pan, melt butter over medium heat. Stir flour into butter and cook 2 minutes on medium heat, stirring constantly. Gradually whisk milk into flour mixture and cook until thickened, stirring constantly. Reduce heat to low and stir in cheeses, onion powder, dry mustard and pepper. Stir in cooked pasta.
Divide evenly into prepared pans. Bake 15 minutes or until bubbly. Cool in pans 15 minutes.
Meanwhile, in saucepan, heat chili according to package directions. Serve each macaroni cup on top of 1/4 cup chili.
Tip: To make ahead, refrigerate macaroni and cheese cups in muffin pans after baking. When ready to serve, remove from pans and microwave 30-45 seconds each until heated through.