From what i have so far seen in the Embedded Jopr, this isn't available. The main reason i guess is because if you deploy the app to an external folder then the admin console should through an API let the Profile service configuration know about this new location so that on a server restart, that new location is checked for application deployments. I don't know whether such API exists. Maybe someone from the embedded jopr team will be able to confirm.
I actually have declared my other directory in the BootstrapProfileFactory. And admin-console is able to undeploy the applications that I put in this directory.
I found something which looks like such a choice in the notes of admin-console.war/plugins/jopr-jboss-as-5-plugin-2.3.0.EmbJopr.1.2.0-1.jar/META-INF/rhq-plugin.xml (simple-property deployDirectory). But I wasn't able to make it work...