No, why are they forced to make this specific choice? Why would they need to deduct time from their lunch break in order to use the bathroom? Using the bathroom and eating lunch are not normally mutually exclusive activities, unless there is a third party enforcing such an exclusion.
Sorry, we might be talking past one another. When I hear about peeing in bottles, I think of the delivery drivers. This is the obvious place bottles would get used, and in my recollection this was most of the reporting on the pee bottles. I believe there was also reporting on workers in the brick and mortar fulfillment center using bottles to meet their quotas, which is perhaps what you are talking about.
For delivery routes, there's no simple solution for bathroom access (unless you want to talk about installing some step up from a "bottle" in all the vans). Meaning a driver will inevitably have to choose to spend time not delivering packages to leave the van and use an indoor bathroom.
If you are talking about the workers at the fulfillment centers, I do agree that is indefensible. That human need should be entirely owned by the business. If it takes workers too long to walk to the bathroom, or if Amazon insists on using time with security lines and whatnot, that's entirely on Amazon.
(Also to each their own, but using the bathroom and eating lunch are definitely mutually exclusive activities for me)