Marsala and Mushroom Pasta Bake

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Kosher salt and freshly cracked black pepper

1 pound cavatappi pasta

6 tablespoons unsalted butter

6 cups sliced mixed mushrooms (shiitake and cremini)

1 medium yellow onion, thinly sliced

2 cloves garlic, minced

1 tablespoon finely chopped fresh thyme

1/3 cup all-purpose flour

1 cup marsala wine

3 cups vegetable stock

1 cup whole milk

Freshly grated nutmeg

1/2 cup finely chopped fresh parsley

2 cups shredded mozzarella cheese

1/4 cup freshly grated Parmesan