The host controller logic for creating the boot operations for a server isn't dealing with deployments or system properties.

addSocketBindings(updates, portOffSet, socketBindingRef);

addSubsystems(updates);
//TODO deployments
// TODO system properties
return updates;

When fixing this, check the status of JBAS-9147, since the ideal operations to generate depend on whether that's done (i.e. deployment "add" w/ "enabled"=>true vs "add" + "deploy")