When I have used the batch printing in the past, it funnels all printing through Creo View which allows you access to the print driver for settings. If I remember correctly, you could print single or groups of items with different print settings.
Unfortunately, this option is not available for items published to PDF. (Eager to be corrected on this point... anyone, anyone?)
While we're on the subject, there is a batch print option from each context that can be run from the server instead of the client. See batch print in the help system.
All the best,
Jered
Ps. For the initial step of transposing a list of items from a column to a row, notepad++ has a command to join lines which handles this easily. Follow this up with find/replace... (this process can also be macro'd into a single command).