Print Organizer does not currently support ustation.exe command-line workspace customization, although a priority build might be available that adds that capability via a configuration variable. Bentley Support can offer more information on that. Refer to CR 262657.
In the commercial release, you would need to remove the command-line options and launch ustation.exe normally (which is how Print Organizer launches its background MicroStation process). You could modify the standard mslocal.cfg to use your customized settings.
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You can still run the Batch Print cmd, mdl load batchplt.
You can put Batch Print cmd in a key-in, or as a modification to "File" as a site/network task dgnlib pointed to by MS_GUIDGNLIBLIST.