I have JVM running  in WAS 8.5.5 and I have the SERVER_LOG_ROOT  set to my choice. Now there is an application installed on this JVM which is using log4j to write application logs, it has something like this ${server.log.root}/application.log set in the log4j.xml file.  I do not have this variable defined in the environment variables or a custom property, but  the application log files are being written to the  profile home directory which /opt/IBM/WebSphere/AppServer/profiles/name/application.log.
when I look for the details on the  process id  I see -Dserver.root  set but not the server.log.root. Any idea where this value for server.log.root picked up from ?