There is a way to set the value for INSTALLDIR through the Repackager IDE. You can do this in the Captured Installation view - Original target folder setting. You may need to save and close and reopen the Repackager IDE to make sure this setting sticks.
We have fixed a bug so that it will be easy to change INSTALLDIR when using InstallShield Editor to edit an ISM file created by Repackager. Until this fix gets released, you can always open the ISM with InstallShield and go to the Direct Editor view and edit the Directory table to get your desired INSTALLDIR setting. This is a bit more advanced and requires understanding the slightly complicated Directory table structure.