Preheat the oven to 425°F (220°C).
Heat the olive oil in a large oven-safe skillet over medium-high heat until shimmering.
Add the ground meat and chopped onion and cook, breaking the meat into pieces, until browned, about 5 minutes.
Stir in the chopped jalapeños, minced garlic, smoked paprika, ground cumin, and kosher salt; cook for 1 minute until fragrant.
Add the red enchilada sauce and the chopped chipotle (if using), then add 2 cups of water and bring the mixture to a boil.
Stir in the dry rice, cover with the skillet lid, reduce heat to the lowest setting, and simmer for 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, top with the tortilla chips pressing them gently into the cheese, then evenly sprinkle the remaining cheese on top.
Transfer the skillet to the preheated oven and bake for 10 minutes, until the cheese is melted.
Serve topped with sliced avocado, extra cilantro, and a dollop of yogurt as desired.