I don’t eat at Chipole but maybe I don’t understand the process. Every other fast food place requires you to pay when you place your order, before you get the food. Insisting on that would be the best course of action.
To reduce wait time, modern restaurant management systems start the order in the kitchen *as the order is entered*. The desired end result is that the customer gets their order just as they get their payment in or as close to that as possible.
The last time I was at a Chipotle (years ago) you get in a line like in a cafeteria, sliding your tray along as you tell them what you want on your wrap or salad. At the end of the line is the cash register where you pay, adding your chips, drinks, etc.
So after your food is all prepared to your order, THEN you pay.
Subway is the same way.