Preheat the oven to 425°F (220°C).
Heat 2 tablespoons olive oil in a large oven-safe skillet over high heat until shimmering.
Add the ground meat and chopped onion; cook, breaking up the meat, until browned, about 5 minutes.
Stir in the chopped jalapeños, minced garlic, smoked paprika, ground cumin, and kosher salt; cook 1 minute until fragrant.
Add the enchilada sauce, chopped chipotle if using, and 2 cups water; bring to a boil.
Stir in the dry long-grain rice, cover the skillet, reduce heat to the lowest setting, and simmer 15 minutes until most of the liquid is absorbed but rice is not fully dry.
Remove the skillet from heat and stir in the chopped cilantro and lime juice.
Sprinkle one-third of the shredded cheese over the rice mixture, add the tortilla chips on top pressing gently into the cheese, then evenly sprinkle remaining cheese.
Transfer the skillet to the preheated oven and bake about 10 minutes until the cheese is melted and bubbly.
Serve topped with sliced avocado, extra cilantro, and a dollop of yogurt as desired.
