Is it possible (with adminstudio) to re-package an installer that already relies on an .msi file?

I have some apps that run setup.exe's to launch an MSI file. when I put them into adminstudio repackaging wizard, it says "this is already an msi file, you shouldnt do this, use the tuner instead"..

Since ZCM doesnt handle large amounts of files in a bundle very well, I'd like to convert apps from multiple files called from an msi, to a single, larger msi file.

Is it possible? if so , what are the right steps to take?

i.e. groupwise is an example of an application that has a small msi file that relies on a ton of other files in the directory.