Resolution:
When you register EMS Plugin using domain utility, it uses tibjmswrapper to generate the script and .tra file for EMS server under:

TIBCO_HOME/tra/domain/&ltdomainName>/application/TIBCOServers

Wrapper that is running in the background provides all the microagents that ems instance needs.  Wrapper communicates with EMS to get the requested data. When you start the ems instance from Admin, you would see the wrap and EMS server started.

This EMS instance will associate the appropriate microagents which are responsible for showing the status in Admin GUI. If users start the EMS server through Admin GUI, it will invoke the scripts in the Admin directory to show the status. If it is not started from the Admin GUI, it will not show the correct status as the EMS instance does not have the appropriate microagent.