Yes, the script logic would be lost as well. At its core, the normal repackaging process is agnostic to the installation technology the original setup was built with:
Installation Monitoring simply hooks the running process to see what changes it makes to the OS (Think RegMon and FileMon)
Snapshot looks at the base state of the OS, and then the changes made afterward, and builds a package off of the differences between the two.
There's also the 'InstallShield Professional Logging' method, which reads the *.ilg file to preserve things like path variables and feature trees:
http://helpnet.macrovision.com/robo/projects/adminstudio80/ISRConceptRepackagingMethodsProEngine.htmAnd then the InstallScript Scan (which you might be prompted for sometimes) is designed for converting an InstallScript MSI project to a Basic MSI project without changing any of the Component Codes, Upgrade Code, Product Code, etc. This process specifically removes the custom InstallScript dialogs.
So in short, none of these things preserve the installscript code you started with. If you'd like to include this in the repackaged output, you'll need to drop this into the resultant editor project.