In a large skillet over medium-low heat, melt 2 tbsp butter and 1 tbsp olive oil. Add sliced onions and a pinch of salt. Cook slowly for 30-45 minutes, stirring occasionally, until deep brown and jammy. Add thyme, then deglaze with beef broth, scraping the pan bottom. Set aside.

Cook pasta in salted boiling water until al dente (1-2 mins less than package directions). Drain. In a separate saucepan, melt 1/4 cup butter over medium heat. Whisk in flour and cook for 1 minute. Slowly whisk in milk until smooth. Cook until thickened. Remove from heat and stir in shredded cheeses until melted. Season with salt, pepper, and nutmeg.

Preheat oven to 375°F (190°C). In a large bowl, combine the cooked pasta, cheese sauce, and caramelized onions. Pour into a 9x13 inch baking dish. In a small bowl, toss Panko with 2 tbsp melted butter and sprinkle over the pasta.

Bake for 20-25 minutes until bubbly and the topping is golden brown. Let rest for a few minutes. Garnish with fresh parsley before serving.