Step 1: Roast the poblano peppers. Preheat your oven broiler or grill. Place poblanos on a baking sheet or directly over a flame. Roast, turning occasionally, until the skin is charred and blistered on all sides (about 5-8 minutes).
Step 2: Steam and peel peppers. Transfer the hot peppers to a bowl and cover tightly with plastic wrap or place in a paper bag for 10-15 minutes. This steams them, making peeling easier. Once cooled, peel the skin, remove stems, seeds, and membranes. Slice the peppers into 1-inch wide strips.
Step 3: Prepare the sauce. In a large skillet, heat olive oil over medium heat. Add chopped onion and cook until softened, about 5-7 minutes. Add minced garlic and cook for 1 minute more until fragrant. Stir in diced tomatoes (undrained), diced green chiles, ground cumin, oregano, salt, and pepper. Bring to a simmer and cook for 5-7 minutes, allowing flavors to meld. Remove from heat.
Step 4: Prepare egg mixture and preheat oven. In a medium bowl, whisk together eggs, milk, and flour until smooth. Preheat oven to 375°F (190°C). Lightly grease a 9x13 inch baking dish.
Step 5: Assemble the casserole. Spread half of the poblano strips evenly over the bottom of the prepared baking dish. Top with half of the shredded Monterey Jack and cheddar cheese. Pour half of the tomato sauce mixture over the cheese. Repeat layers: remaining poblano strips, remaining cheese, and then pour the egg mixture evenly over the top.
Step 6: Bake the casserole. Bake for 35-40 minutes, or until the casserole is bubbly, the cheese is melted and golden, and the egg mixture is set. If the top browns too quickly, you can loosely tent with foil.
Step 7: Rest and serve. Remove from oven and let the casserole rest for 5-10 minutes before serving. Garnish with fresh chopped cilantro and serve with optional sour cream or Mexican crema.