The checkboxes in the GUI that you refer to save your BLA preferences to a snapshot filter within the server profile. You can specify that this filter should be used during a CLI operation using the "-filter" argument on the runDeliver command:
runDeliver -mode preview -profile <path_to_server_profile> -tokens "Default Tokens" -filter <filter_name> -config <path_to_configuration>
Let me know if that helps.
Lead Tech Support Analyst
BladeLogic Application Release Automation
Thanks Anthony that was it.