Yes, this can be done. To achieve this you can use a little trick and please keep in mind that it is recommandable to use a clean machine.
You must use a dummy exe (i.e. NOTEPAD.EXE) for the "Application Path" when the Repackager wizard starts. After the wizard will launch the NOTEPAD.EXE you should perform your custom operation, for example configuring your printer settings. After that close the NOTEPAD.EXE and continue with the Repackager wizard .