The setRepo command provides an option that allows you to specify an arbitrary set of properties. The -D $propertiesFilePath option allows you to specify any number of settings, including vendor-specific properties not specified by JNDI, by including them in a properties file that you create.
For example, to specify a different JNDI port number, include a line like the following in your properties file:
java.naming.provider.url=iiop://localhost:2909