I have safely eaten at several chipotle's...
HOWEVER, when I went in to order, I told them straight up that I needed Gluten Free and it wasn't a preference. She got clean utensils, and got ready to make my order when I noticed she grabbed the soft tortillas.
I asked her "are you sure those are the gluten free ones?"
She replied with "I'm not sure. I think so. It doesn't say the ingredients on the package."
I then walked out. I wasn't about to risk being sick!!
They are pretty good about cross contamination. When mentioning celiacs they brought out fresh items for my bowl and got new utensils for them as well. I don’t know how well they are when you order online but in person they pay good attention. Again, it is a chain so experiences will vary based on the workers there. I didn’t have a reaction afterwards!
About the same experience as every other chipotle location, maybe slightly better than average. They will change their gloves. I personally stopped asking for fresh ingredients from the back and just avoid the lettuce and shredded cheese all together. I haven’t had an issue and have eaten there many times. If you want to be extra cautious you can ask them to use fresh ingredients from the back, especially if you’re getting the lettuce or shredded cheese because they touch those with their gloves.