Preheat the oven to 425°F (220°C).
In a large bowl, combine 1 1/2 pounds boneless chicken breasts or thighs, 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. Toss until the chicken is evenly coated.
Spread the coated chicken in a single layer on a rimmed baking sheet. Scatter the 2 sliced bell peppers and the sliced yellow onion evenly around and on top of the chicken.
Bake 20–25 minutes, until the chicken is cooked through (165°F internal temperature) and the peppers and onions begin to char at the edges.
Remove the sheet pan from the oven. Use two forks to shred the chicken right on the pan, then toss the shredded chicken with the pan juices and vegetables so everything is well coated.
While the chicken bakes or after you remove it from the oven, make the avocado-jalapeño salsa: in a bowl, gently combine 2–3 chopped avocados, the 1 jalapeño (seeded if desired) chopped, 1/2 cup chopped fresh cilantro, and 1/4 cup lime juice. Season to taste with flaky salt and toss gently.
Divide 3–4 cups cooked rice among bowls. Top each bowl with the shredded chicken and roasted peppers/onions from the pan.
Sprinkle 1 cup shredded cheddar/cotija cheese over the bowls. Add spoonfuls of the avocado-jalapeño salsa, a dollop of yogurt or sour cream, and serve with limes for squeezing. Finish with flaky salt to taste.