Preheat the oven to 425°F (220°C).
In a medium bowl combine 3/4 cup red enchilada sauce, 2–3 chopped chipotle peppers in adobo, 1 teaspoon dried oregano, 1 teaspoon ground cumin, and 1 teaspoon salt. Stir to make the sauce.
Place the 1 1/2 pounds boneless chicken breasts or thighs on a rimmed baking sheet. Pour the sauce over the chicken and turn the pieces to coat evenly.
Add the 2 sliced bell peppers and 1 sliced yellow onion to the baking sheet, arranging everything in a single layer around the chicken. Sprinkle a little flaky salt over the peppers and onion if desired.
Bake 20–25 minutes, until the chicken is cooked through and the peppers begin to char (internal temperature for chicken should reach 165°F/74°C).
Remove the baking sheet from the oven. Transfer the chicken to a cutting board and shred with two forks. Return the shredded chicken to the baking sheet and toss it with the pan sauce and roasted peppers/onions to combine.
Meanwhile, make the avocado salsa: in a bowl gently toss together 2–3 chopped avocados, 1 chopped jalapeño (seeded if desired), 1/2 cup chopped fresh cilantro, and 1/4 cup lime juice. Season with flaky salt to taste.
To assemble bowls: divide 3–4 cups cooked rice among bowls. Top each bowl with the chicken, peppers, and onions from the sheet. Sprinkle with 1 cup shredded cheddar or cotija cheese. Add spoonfuls of the avocado salsa, a dollop of yogurt or sour cream, and squeeze fresh limes over each bowl. Finish with a pinch of flaky salt and serve.