The ConfigurationElement embeds Jetty's proprietary configuration file into JBoss jboss-service.xml dd.
Webapps deployed via Jetty's config will not benefit from the JBoss integration, as they bypass it.
To take advantage of all the integration features e.g. ENV, JBoss aware JSP classpath etc, you MUST deploy webapps in the JBoss way.
If you want to maintain the tree outside the deploy dir, you should be able to set up a path to it using one of the deployer MBeans - I haven't tried this for a while.
Report back with your findings and I will put them in my FAQ.