The best way of customising an installation that uses the isScript engine (a Standard MSI or InstallScript MSI project) is at design time, modifying the script and logic coded into the project.
Using a Transform causes a number of issues to be considered and the process is not recommended. The behaviour may not be reliable depending on the logic affected. You may have come across the KB article which discusses the process of disassociating the MSI file from the Setup.exe, Q108166 "HOWTO: Deploy an MSI Wrapped with an InstallShield Script-Based Setup.exe."
http://support.installshield.com/kb/view.asp?articleid=Q108166 While this will allow Tuner to generated a Transform, it only takes into account the MSI tables and ignores the scripted logic in both the dialogs and the functions.
The bottom line is that using a Transform with an InstallScript MSI project may work for the most simple of projects but it should not be relied upon as a fool-proof method.