David,

From the manual:

"Unlike the monolithic installation technologies available today, SetupBuilder 6 has been designed from the ground up to deliver a perfect fusion of installation authoring, web deployment, configuration management, and scripting technologies. When MSI is simply not enough...use SetupBuilder 6."

In other words, SetupBuilder 6 compiles high-performance, low-overhead, native Windows executables.

-But- <g> from the "What is Planned for Future Versions" section:

"Microsoft Windows Installer (MSI) compiler (SetupBuilder 7). Create native Microsoft Windows Installer installations."

And finally this one:
http://www.lindersoft.com/forums/showthread.php?t=4111

Does this help?

Friedrich