Beat egg and egg whites in a small bowl. Mix in Parmesan cheese, Cheddar cheese, salt, red pepper flakes, garlic powder, nutmeg, and pepper.
Heat oil in a large skillet over medium heat; cook and stir mushrooms, green onion, and bell pepper until tender, about 5 minutes. Place spinach in skillet and cook until just wilted. Stir in diced tomato and egg mixture; as eggs set, lift edges, letting uncooked portion flow underneath. Cook until egg mixture sets, 10 to 15 minutes; cut into wedges and serve immediately.