Preheat oven to 400°. Cook pasta according to package directions in a large pot of boiling, well-salted water until tender to the bite, 7 to 12 minutes. Drain, but do not rinse.
In a large frying pan over medium-high heat, melt 2 tbsp. butter. Add shallots and cook until light golden, about 3 minutes. Sprinkle shallot-butter mixture with flour; cook, stirring often, 1 minute. Add wine and stir, picking up any browned bits from the bottom of the pan. Add cream and stir well. Sprinkle in cheeses, one large handful at a time, stirring until each handful is mostly melted before adding the next. Stir in 2 tbsp. chives, mustard, 1/4 tsp. salt, cayenne, and nutmeg. Stir cooked pasta into cheese mixture, then pour all into a 2-qt. baking dish.
In a food processor, pulse bread with remaining 1 1/2 tbsp. butter, 1 tsp. chives, and 1/4 tsp. salt until coarse bread crumbs form. Sprinkle bread crumbs over pasta and cheese and bake until top is browned and cheese is bubbling, 15 to 20 minutes.
Note: Nutritional analysis is per serving.