Preheat broiler. Line a baking sheet with aluminum foil and lightly brush with oil or spray with cooking spray. Arrange onion, peppers, and garlic in a single layer, and broil for 5 to 10 minutes or until peppers and onions are softened and starting to blister (if the peppers are cooking quicker than the onions, you may want to remove them from the baking sheet and cook the onions a little bit longer).
Transfer onions, peppers and garlic to a blender along with canned tomatoes. If you prefer a chunkier sauce, only add half the tomatoes, reserving the rest to add back after blending. Purée until smooth. Pour into a saucepan and set over medium heat. Bring to a simmer and let bubble, stirring regularly to avoid splattering, for 10 minutes. Season to taste with salt and pepper.
Preheat oven to 400 degrees F. Lightly oil a cast-iron skillet or other oven-safe pan. Arrange a layer of tortilla chips in pan. Drizzle with about 1/4 cup of sauce sauce, then sprinkle with half of shredded cheese and half of cotija cheese. Top with another layer of tortilla chips, and repeat.
Bake for 5 to 10 minutes or until cheese is melted and bubbly.
Meanwhile, preheat a nonstick skillet over medium heat. Whisk eggs until uniform in color. Add butter to hot skillet until melted and sizzling, then add eggs. Let cook for 30 seconds, then start scraping the bottom of the pan with a spatula, flipping the cooked pieces of egg so the uncooked parts come in contact with the pan. Continue scraping and flipping for another 1-2 minutes, breaking up any large pieces of egg, until just cooked through.
Remove skillet from oven and spoon scrambled eggs over top. Scatter jalapeño and radish slices over top, sprinkle with cilantro, and finish with a generous dollop of sour cream in the middle. Serve immediately.