In a large skillet over medium heat, warm the oil until sizzling. Add the onion, 1 teaspoon salt and 1/4 teaspoon pepper, then cook, stirring occasionally until browned, about 5 minutes. Add the garlic, oregano, and cumin, then cook, stirring for 30 seconds. Remove from the heat, then transfer 1/2 cup of the mixture to a large mixing bowl; set aside the skillet with the remaining mixture. Line a rimmed baking sheet with parchment paper.
Into the bowl with the onion mixture, stir in the panko and 1/2 cup water. Let stand until the panko softens, about 5 minutes. Using a spatula, mash the mixture to a paste, then add the beef, 1/2 cup cilantro and 1 teaspoon of salt and pepper. Mix well, then divide into 16 two-tablespoon portions, rolling each into a ball and placing on the prepared baking sheet. Cover and refrigerate for 15 to 30 minutes. Meanwhile, heat the oven to 450 F with a rack in the middle position.
Uncover the meatballs and roast until browned and the centre reaches a temperature of 160 F, 12-15 minutes. Remove from the oven and set aside.
To the skillet with the remaining onion mixture, stir in the tomatoes and 1/2 cup water. Bring to a simmer over medium high, then add the chipotle chilies and cook, stirring occasionally, until a spatula drawn through the sauce leaves a trail, about 3 minutes. Taste and season with salt and pepper. Add the meatballs and stir gently to coat with the sauce, then stir in the remaining 1/4 cup of cilantro with sprinkle of queso fresco.