Preheat the oven to 400°F (200°C).
Season the cooked spaghetti squash with salt and pepper; if chilled, bring it to room temperature before assembling.
Grease a pie plate with coconut oil, then press the spaghetti squash into the plate and up the sides to form an even crust.
Slice the tomatoes and lay them on paper towels to drain while you cook the other vegetables.
Heat the olive oil in a large skillet over medium heat; sauté the zucchini, diced red bell pepper, and sliced red onion until tender, about 4–6 minutes. Remove from heat and let cool briefly.
In a mixing bowl, whisk together the eggs, coconut milk, 1/2 teaspoon salt, dry mustard, ground black pepper, and garlic powder, then stir in half of the sliced basil.
Temper the egg mixture by whisking in one spoonful of the hot vegetables at a time until combined, then fold in the remaining vegetable mixture.
Arrange half of the tomato slices in the bottom of the spaghetti squash crust, pour the egg and vegetable mixture into the crust, then top with the remaining tomato slices.
Bake in the preheated oven until the center is set and the crust is crisp, about 30–45 minutes; check for doneness by gently tapping the plate—the center should no longer be jiggly.
Remove from the oven, sprinkle with the remaining basil, slice, and serve warm.
