Resolution:
For the system properties to be reflected, they need to be passed using the custom property in the be-engine.tra file (java.extended.properties).

So, in your be-engine.tra file, you can add something like  -
java.extended.properties= -Duser.region=DE -Duser.language=de

If you want to get this property in the TIBCO Admin GUI before deployment, please do the following -
- Before creating your EAR,
edit $TIBCO_HOME\be\2.0\lib\com\tibco\deployment\be-engine.xml
Here add the following property:
     &ltproperty>
       &ltname&gtExtended Properties</name>
       &ltoption&gtjava.extended.properties</option>
       &ltdefault></default>
       &ltdescription&gtDefines java extended properties</description>
     </property>

- Open Designer and create an EAR(whenever you create an EAR, this additional property will be included which in turn gets reflected in the TIBCO Admin GUI)