Preheat Oven and Prep Dish: Arrange an oven rack in the center position and preheat your oven to 360°F (180°C). Lightly grease your 9x9 inch or 11x7 inch baking dish with nonstick spray or olive oil.
Sauté Mushrooms: Heat the olive oil in a large skillet over medium-high heat. Once hot, add the sliced mushrooms in a single layer if possible (cook in batches if necessary to avoid crowding). Cook, stirring occasionally, until browned and tender, about 3-5 minutes.
Wilt Spinach and Aromatics: Add the minced garlic and packed spinach leaves to the skillet with the mushrooms. Stir continuously until the spinach wilts down significantly, about 2-3 minutes. Stir in the dried thyme. Remove from heat and season lightly with salt and pepper.
Layer Vegetables and Cheese: Spread the cooked mushroom and spinach mixture evenly across the bottom of the prepared baking dish. Scatter the sliced green onions over the vegetables. Crumble about half (1.5 oz) of the goat cheese evenly over the vegetable layer.
Prepare Egg Mixture: In a large bowl, crack the 13 large eggs. Add the 6 tablespoons of milk, the pinch of ground nutmeg, ¼ tsp salt, and ¼ tsp pepper. Whisk vigorously until the eggs and milk are well combined and slightly frothy.
Combine and Top: Pour the egg mixture evenly over the vegetables and goat cheese in the baking dish. Crumble the remaining half (1.5 oz) of the goat cheese over the top of the egg mixture.
Bake: Place the baking dish in the preheated oven. Bake for 30 to 35 minutes, or until the eggs are fully set (no longer jiggly in the center) and the edges are lightly golden.
Rest and Serve: Carefully remove the casserole from the oven and let it cool for at least 5 minutes before slicing into squares. Serve warm. Leftovers store well in the refrigerator for 3-4 days.