In later versions of Bamboo (Bamboo 5.1 and Newer) Tomcat replaced Jetty as the standalone app server. This means that the way Bamboo is started, stopped and upgraded has changed. In Tomcat, all the system default settings are set in the bin/catalina.bat and supplementary changes are made via the setenv.bat file under <bamboo-installation-directory>/bin as explained here: Configuring Bamboo on Start-Up. For Bamboo running as a service though, properties other than java_opts can be set via the bin/service.bat file.

To set user profile parameters (Ex: HOME=%USERPROFILE%,  HOMEPATH=%USERPROFILE%), it will be automatically determined by the user running the bamboo service. So if you want to run as a specific profile, you need to set the service to run with that profile (Please refer to this page for more details: Running Bamboo as a Windows Service).