Season the chicken with cumin, smoked paprika, garlic powder, onion powder, oregano, salt, and black pepper and toss to coat evenly.
Heat oil in a large deep skillet or wide pot over medium-high heat. Add the chicken and sear undisturbed for 2–4 minutes until golden on the bottom, then flip and cook another 2-4 minutes until just cooked through. Transfer to a plate and set aside, do not wipe the pan.
Reduce heat to medium and add the roughly chopped onion to the same pan, scraping up all the browned bits from the chicken as you go. Cook for 3 minutes until softened.
Add the garlic and cook 30 seconds more until fragrant. Add the Roma tomatoes and cook for another 2–3 minutes until they start to break down and release their juices. Remove from heat and let cool slightly.
Transfer the onion, garlic, and tomato mixture to a blender. Add the chipotles, adobo sauce, Alta Dena Protein Milk, chicken broth, and cream cheese and blend on high until completely smooth and creamy.
Pour the blended chipotle cream base back into the same pan and stir, scraping up any remaining bits from the bottom. Bring to a gentle boil.
Add the dry pasta directly into the liquid, fanning it out and pressing it down so it is fully submerged. Cover and cook over medium heat for 10–12 minutes, using tongs to toss and separate the pasta every 2–3 minutes so it cooks evenly and nothing sticks to the bottom. By the end the pasta should be al dente and the sauce reduced to a creamy glossy consistency that clings to every strand - not soupy, not dry.
Reduce heat to the lowest setting and add the shredded mozzarella cheese and ground cotija, tossing with tongs until completely melted and the sauce is thick and creamy. If the sauce looks too thick add a splash of warm milk and toss until you reach the perfect consistency. Taste and adjust salt.
Slice the seared chicken and serve on top of the pasta. Garnish with fresh cilantro and a dusting of ground cotija and serve immediately.