Preheat the oven to 400°F (200°C). If the cooked spaghetti squash is chilled, let it come to room temperature.
Season the cooked spaghetti squash with salt and pepper and press it evenly into a greased 9-inch pie plate, pressing up the sides to form a crust.
Arrange half of the sliced tomatoes in an even layer on the bottom of the squash crust and set the remaining slices aside on paper towels to drain.
Heat the olive oil in a skillet over medium heat, then sauté the zucchini, diced red bell pepper, and sliced red onion until tender, about 5–7 minutes. Remove from heat.
In a mixing bowl, whisk the eggs with the coconut milk, 1/2 teaspoon salt, dry mustard, black pepper, and garlic powder until combined. Stir in half of the sliced basil.
Temper the egg mixture by whisking in one spoonful of the hot sautéed vegetables at a time, then fold the warmed vegetables into the egg mixture.
Pour the egg and vegetable mixture into the squash crust over the tomatoes. Top with the remaining tomato slices arranged evenly.
Bake in the preheated oven until the center is set and the squash crust is slightly crisp, about 30–45 minutes; start checking at 30 minutes.
Remove from oven, sprinkle with the remaining basil, let rest a few minutes, then slice and serve.