Generally, with what's called "Pure InstallScript Projects", you have a limited ability to account for whatever bad behavior the original setup developer authored into it. (Less so with 'InstallScript MSI') So the case may be that repackaging is the way to go.
What I would typically recommend in a case like this is check to see if possibly the setup.exe file contains an MSI file. If it does, then you might be able to track down what's popping up the dialog, and remove or otherwise account for it.
If not, then the way to handle it would be to see if you can identify how to put the application in a working state manually after installing the MSI, and integrate those steps into your repackaged project.
