Resolution:
TIBCO Administrator 5.4, TRA 5.5 introduced the concept of creating Admin Domain that uses EMS instead of RV. Here are the steps that needs to be followed to add BWC 5.4 server to such domain -

- Installed TRA 5.5, Administrator 5.4, EMS 4.4, BW 5.4, BWC 5.4 and BWFB 5.2.

- Created Admin Domain that uses EMS instead of RV and I think EMS based domains requires DB repository for the Admin Domain, so used this.

- Started and Tested Admin Domain and Hawk Agent works well.

- Added BWC Server and BWC Document repository server to the Domain and it was successful.

- From Admin GUI, started BWC Servers and it works, also synchronized users and was successful.

- Created Production Mode Platform war and added Tomcat instance to Domain, it worked.

- Started Tomcat instance and tried deploying DefaultDesktop and it failed with same error as you saw: Caused by: java.lang.IllegalAccessError: tried to access field com.tibco.tibrv.Tibrv._impl from class com.tibco.tibrv.TibrvJMSTransport

- Added JMS jars to the CLASSPATH in the tomcat startup .tra file and those errors could be resolved.

In theTomcat start-up .tra the classpath should look something like this -
tibco.class.path.extended=C\:/tibco/ems/clients/java/jms.jar;C\:/tibco/ems/clients/java/tibjms.jar;C\:/tibco/ems/clients/java/tibrvjms.jar;C\:/tibco/bwc/5.4/tomcat/bin/bootstrap.jar;C\:/tibco/jre/1.5.0/lib/tools.jar;C\:/tibco/bwc/5.4/hotfix/lib/icjava720.jar;C\:/tibco/bwc/5.4/lib/icjava720.jar;C\:/tibco/bwc/5.4/deployment/dependency/BWWFlib.jar;C\:/tibco/bwc/5.4/deployment/dependency/BWlib.jar;C\:/tibco/bwc/5.4/deployment/dependency/TRAlib.jar;C\:/tibco/bwc/5.4/deployment/dependency/HAWKlib.jar;C\:/tibco/bwc/5.4/deployment/dependency/RVlib.jar;C\:/tibco/bwc/5.4/deployment/dependency/TPCLlib.jar;C\:/tibco/bwc/5.4/deployment/dependency/TOMCATlib.jar;C\:/tibco/tra/5.5/lib/TIBCrypt.jar;C\:/tibco/tpcl/5.5/tomcat/common/lib/servlet.jar;C\:/tibco/hawk/lib/activation.jar;C\:/tibco/hawk/lib/mail.jar;C\:/tibco/tpcl/5.5/ant/lib;C\:/tibco/tpcl/5.5/jdbc;C\:/tibco/tpcl/5.5/lib/entrust;C\:/tibco/bwc/5.4/deployment/dependency/FORMlib.jar;C\:/tibco/tpcl/5.5/tomcat/server/lib/jakarta-regexp-1.2.jar

How to add and use TIBCO BusinessWorks Collaborator (BWC) 5.4 services with EMS based Admin Domain?