Chipotle's current allergen information identifies milk in shredded Monterey Jack cheese, queso, and sour cream. Leaving those toppings off narrows the ingredient concerns, but it doesn't answer how the nearby bins, serving utensils, gloves, or work surface were handled. You'll want to review the full build and the line setup before deciding.
Chipotle's current allergen chart identifies soy in Sofritas, the tofu-based protein. Choosing another protein removes that identified component from your build, but it doesn't resolve possible contact from the Sofritas pan, serving utensil, gloves, or work surface. You'll have a clearer conversation if you name Sofritas and ask how the protein area is handled.
Chipotle's flour tortillas are the direct wheat concern on its current allergen page, so a burrito or soft flour taco starts with a confirmed conflict. A bowl, salad, or corn-tortilla build changes that ingredient question, but it doesn't answer contact from flour tortillas on gloves, utensils, or the work surface. You'll still want to discuss wheat specifically rather than relying only on gluten-related menu language.