It always will be in MinePeon.
There is an old standard in Unix/Linux that all time/dates on a server OS are in GMT (Or UTC) if you prefer, and since I am an old Unix/Linux guy it is a standard that I still adhere to (Modern Desktop Linux OS's don't anymore). Its all about working in a synchronized timezone no matter where your server is etc... (quite a few internet services log files work in GMT regardless of what you set it to, look at qmail or ftp for example)
Its only when it gets to the application layer where you interact with users that TimeZone is important and that is why you can set it through the WebUI and that setting is used at the application layer.
It wont hurt it though if you set it at the OS level manually, just make sure that you set it in the WebUI as well .
Neil