Preheat your oven to 375°F (190°C). Place the unbaked 9-inch pie crust into a pie dish. If you desire a crispier crust, you may blind bake it for 10-15 minutes before filling, but this is optional.

In a large skillet, melt the butter over medium-low heat. Add the thinly sliced Vidalia onions. Cook slowly, stirring occasionally, for 15-20 minutes, or until the onions are very soft, translucent, and lightly golden. Avoid browning them too much to preserve their sweetness. Remove from heat and let cool slightly.

In a large mixing bowl, whisk together the heavy cream, whole milk, eggs, all-purpose flour, salt, black pepper, and nutmeg (if using) until the mixture is well combined and smooth.

Gently stir the cooled, sautéed Vidalia onions and the shredded Gruyère cheese into the prepared cream mixture.

Pour the entire filling mixture evenly into the unbaked pie crust in the dish. Sprinkle the grated Parmesan cheese over the top of the filling.

Carefully place the pie dish on a baking sheet (to catch any potential drips) and bake in the preheated oven for 45-55 minutes, or until the top is golden brown and the center is set (a knife inserted near the center should come out clean). If the crust edges or top start to brown too quickly, you can loosely tent the pie with aluminum foil.

Once baked, remove the pie from the oven and let it cool on a wire rack for at least 15-20 minutes before slicing and serving. This resting time allows the custard to fully set, making for cleaner slices.