Preheat oven to 400 degrees, and spray a 9×9-inch pan with non-stick cooking spray.
In a medium saucepan, heat 1 tablespoon olive oil. Add onions and spread evenly in pan. Cook over medium-low heat for 3 to 5 minutes, stirring every few minutes, until onions are softened and are a rich brown color.
Combine 1 tablespoon melted butter, bread crumbs, parsley, Parmesan cheese and black pepper in a small bowl.
Fill a large pot with water and bring to a boil. Add penne to boiling water and cook until al dente, about 9 minutes. Drain the pasta.
In a small saucepan, heat 1 teaspoon olive oil over a medium temperature. Add sliced mushrooms and cook until tender, about 5 minutes, stirring occasionally.
In another medium saucepan, melt ¼ cup butter. Add flour and cook for 3 minutes, whisking. Then slowly whisk in the milk until well combined. Bring sauce to a boil, whisking constantly, then reduce heat to low. Add the cream, sour cream, smoked paprika, salt, nutmeg, Emmentaler, Asiago and cheddar. Stir until cheeses are melted and sauce is smooth.
Remove cheese sauce from pan and add in drained pasta. Then stir in the thawed peas, mushrooms, and onion. Transfer pasta mixture to greased baking dish and sprinkle with bread crumb mixture. Bake in the oven until golden and bubbly, about 15 to 20 minutes.