Regardless if the time settings are set to manual or automatic, an updated carrier settings push can change the time settings on a phone whether or not it's been preconfigured by the user or if it's being automatically configured by the network. We open network tickets all the time where I work that deal with this exact issue and there have been many occasions that it happens to be the network that's causing the issue because it's consistently sending a carrier update to the device due to the device not registering that it's fully established on the network due to possible roaming from their home area, or somehow the device is out of range or not properly communicating with the MSC.
Sometimes it's a software issue and a restore will fix it, and sometimes it's a third party application that's causing the device to revert back.
There are many different factors that play into something like this, that it's hard to just immediately assume it's one specific piece of hardware, or software or network push. Just say for instance it's nothing wrong with the phone, but something wrong with software on the device, or something that's being caused by a third party application or maybe a network issue ...
The user reaches out to Apple, gets a new phone, loads everything back onto the device and the issue happens again...
Right back to square one.
It's important to completely troubleshoot all aspects that could be affecting the device, not just randomly assume something is wrong with one specific part of the device and immediately refer them to someone for a replacement. Sometimes, a replacement device can turn out worse than the actual device having the issue.