Preheat oven to 375°F. Grease 1 ½-qt baking dish with 1 T butter and set aside. Melt 3 T butter and stir in breadcrumbs.
Melt remaining 2 T butter over medium heat. Whisk in flour and stir constantly for 1-2 minutes, then slowly pour in warmed milk, whisking constantly to avoid lumps. Continue to cook until mixture is thick, 2-3 minutes. Turn off heat and stir in nutmeg and pepper, then added cheeses and stir to melt. Set aside.
Bring a large pot of salted water to a boil. Add macaroni and cook until al dente. Drain and stir pasta into cheese sauce along with Chobani. Transfer to prepared dish, top with the breadcrumbs and bake until browned, 30 minutes. Cool 5-10 minutes before serving.