When you customize the installer and click on the "Save Package" button/menu item, it requires the setup.ini to include all the changes and the commandline for the transform. You can either extract the exe to the setup.ini or simply save the transform file using Transform > Generate Transform. The later action will only generate the transform and not write anything on setup.ini. In this case the user/admin has to include the parameter for the transform in the command line.
Thanks,
Vinod