Here’s the part you missed... Chipotle prepares each meal custom to the customer. If you get to the register and can’t pay, they will likely have to throw the meal away (or save it for the employee’s lunch... but there are moral hazards to that situation as well). The manager likely wanted the dine-and-dasher to pay before assembly to ensure he wasn’t left with an unsellable meal.
That makes sense. Food waste caused by wannabe dine-and-dashers who are too stupid to realize there is no way to get away with it.