Marinate: Combine chicken, oil, water, and chipotle seasoning in a bowl. Cover and refrigerate for at least 1 hour.
Cook Rice: Rinse the rice until the water runs clear. Cook in a rice cooker or multi-cooker. Once finished, fluff and stir in lime juice and chopped cilantro to taste.
Cook Chicken: Heat a large pan over medium heat. Cook chicken thighs for 5–6 minutes per side until the internal temperature reaches 165°F (74°C). Let rest under foil for 5 minutes, then dice.
Make Guacamole: Mash avocado flesh with half the diced red onion, a handful of cilantro, lime juice, and salt.
Make Pico de Gallo: Toss diced tomatoes, the remaining onion, jalapeño (if using), cilantro, 1/4 cup lime juice, and salt in a bowl.
Assemble: Divide the rice, beans, and chicken into 6 containers.
Serve: Add the cheese, sour cream, pico, and guacamole just before eating to keep the textures fresh.