Preheat the oven to 400°F (200°C). If the cooked spaghetti squash is chilled, bring it to room temperature.
Grease a 9-inch pie plate with coconut oil.
Press the cooked spaghetti squash into the greased pie plate, spreading it evenly and pressing up the sides to form a crust; season lightly with salt and pepper.
Slice the tomatoes and lay the slices on paper towels to drain.
Heat the olive oil in a skillet over medium heat, then sauté the zucchini, red bell pepper, and red onion until tender, about 5–7 minutes; remove from heat and let cool slightly.
In a mixing bowl, whisk together the eggs, coconut milk, 1/2 teaspoon salt, dry mustard, black pepper, and garlic powder, then whisk in half of the sliced basil.
Whisk one spoonful of the hot sautéed vegetables into the egg mixture at a time to temper the eggs and avoid scrambling, then stir in the remaining sautéed vegetables.
Place half of the tomato slices in the bottom of the spaghetti squash crust, pour in the egg and vegetable mixture, then arrange the remaining tomato slices on top.
Bake in the preheated oven until the center is set and the squash crust is slightly crisp, about 30–45 minutes; a gentle tap on the plate should show a firm center.
Garnish the quiche with the remaining basil, slice, and serve warm.