Else, on the user interface side:
Preferences > Attribute Handling > Local Time Zone (or do a find in preferences for "time zone")
for a user to change how Windchill displays the timestamps.
But with your reply, it sounds like you're talking about the timestamp data that gets entered into the database.
I have found that wvs tasks contains incorrect creation time. But after changing the OS timezone all timestamps are looks correct. So in the database all timestamps have an absolute values and UI visualize them with the timezone settings.
The database timezone is GMT.
At a TimeZone.getDefault() level, the method server is also in GMT. The reasons for this are historic dating back to the earliest Java versions.
At a WTContext.getTimeZone() level, however, the method server uses the server OS's timezone as does the server manager (at all levels).
The fact that GMT is used internally in place should not be evident from the UI, etc.