In the "JasperReports Server Installation Manual" section "7.1 Procedure for Installing and Deploying the WAR File in WebSphere", there is a mention of setting JAVA_HOME environment variable as needed. This is false and should actually be discouraged. Java is only needed outside of WebSphere environment to unpack/pack jar filed (section "7.1.2 Preparing JasperReports Server Files"). It is not required to run WebSphere.
Admin should be discouraged to prepare jasperreports-server-5.6-bin.zip file on the server because default_master.properties contains sensitive information. Inastead, jasperreports-server-5.6-bin.zip should be extracted and prepared on admin's administration pc. It is only necessary to specify the database on the remote machine to install the database.
As per instruction, jasperserver.war file is deployed from the WebSphere Management Console web page so there really isn't any need to setup JAVA_HOME on WebSphere server.