Resolution:
If you add additional properties to the be-engine.xml file, located in $TIBCO_HOME/be/3.0/lib/com/tibco/deployment (rebuild the EAR), they do not get put into the TIBCO.xml file inside the BAR and do not show up in Administrator when deployed.

Resolution

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Solution 1). Delete the "be-engine.xml" from <TIBCO_HOME>\be\3.0\hotfix\lib\com\tibco\deployment folder and rebuild the EAR.        
        
Solution 2). Copy the modified "be-engine.xml" to the <TIBCO_HOME>\be\3.0\hotfix\lib\com\tibco\deployment folder and rebuild the EAR.
          
Note that the problem is occurring because there already exists a "be-engine.xml" file in the <TIBCO_HOME>\be\3.0\hotfix\lib\com\tibco\deployment folder. Since it comes before the  <TIBCO_HOME>\be\3.0\lib\com\tibco\deployment folder in the classpath in tra file, it is picking up from the hotfix folder. Also, on comparing be-engine.xml with the hotfix folder and without the hotfix folder being the same, it is an extra file in the hotfix folder and can be deleted or neglected as suggested in the above solutions.

Additional properties added to the be-engine.xml file located in $TIBCO_HOME/be/3.0/lib/com/tibco/deployment do not get put into the TIBCO.xml file inside the BAR, and does not show up in Administrator when deployed.