Heat frying pan over medium heat and add oil and half the butter. Add peppers and onions and saute, tossing to coat. Season with salt and pinch of crushed red pepper flake. Cook until mostly soft, then remove from heat and reserve.
While peppers and onions cook, make egg mixture. Combine whole eggs, egg whites, milk, chili powder, paprika and cayenne in medium bowl. Season with salt and a touch of black pepper. Whisk until well combined.
Put small pot on medium-low heat, and add remaining butter. Pour in egg mixture, whisking as adding to pot. Use rubber spatula to fold eggs and scrape bottom to avoid burning. Remove from heat halfway through to lower temperature of eggs while stirring. Return to heat.
Once it has become more solid than liquid, add back sauteed peppers and onions. Stir to combine. Add nutritional yeast and “cheese”. Fold eggs one more time and remove from heat, plating immediately to avoid overcooking. Season with salt and pepper, and serve.