Hellow Carrara,
There are some needs to call the transactions from the custom reports. Some times user wants to navigate to the transactions from the report output. In that cases we can use this feature calling the transaction from the custom program.
And as you said, if you want to fill the user preferences when calling the tranaction, you can fill the fields using the SET PARAMETER statement before CALL TRANSACTION statement.
Please follow the link to get clear idea on the same: http://scn.sap.com/docs/DOC-30683
Thanks and regards,
Vijay