Prepare the crust: In a large bowl, whisk together flour and salt. Cut in the cold butter using a pastry blender or your fingertips until the mixture resembles coarse crumbs with some pea-sized pieces. Gradually add ice water, 1 tablespoon at a time, mixing until the dough just comes together. Form into a disc, wrap in plastic, and refrigerate for at least 30 minutes.
Preheat oven to 375°F (190°C).
Cook the vegetables: In a skillet, heat olive oil over medium heat. Add the sliced onion and cook until softened and lightly browned, about 8-10 minutes. Add the sliced zucchini and cook for another 5-7 minutes until slightly tender. Remove from heat and let cool slightly.
Assemble the pie: On a lightly floured surface, roll out the chilled dough into a 12-inch circle. Carefully transfer the dough to a 9-inch pie plate. Trim and crimp the edges.
Spread the cooked zucchini and onion mixture evenly over the bottom of the pie crust.
In a separate bowl, whisk together the eggs, milk, cheddar cheese, Parmesan cheese, salt, pepper, and nutmeg (if using) until well combined.
Pour the egg mixture over the zucchini and onion in the pie crust.
Bake: Place the pie on a baking sheet to catch any drips. Bake for 40-45 minutes, or until the filling is set and the crust is golden brown. If the crust edges start to brown too quickly, you can cover them with foil.
Let cool for at least 10 minutes before slicing and serving.