Spray a nonstick skillet with cooking spray. Sauté the onions, red pepper, and garlic over medium-low heat for approximately 4 minutes.
Spray two 2-cup oval casseroles with the cooking spray. Combine the pepper mixture and the bread. Divide into the two casseroles. Situate 3 tomato slices on top of each and sprinkle both cheeses over all.
Whisk the milk, egg substitute, Italian seasoning, dry mustard, pepper, and cayenne pepper in a bowl. Drizzle over the bread, cover with foil, and refrigerate for at least 8 hours.
Bake, uncovered, for about 25 to 30 minutes. Let cool for 5 minutes before serving.