Use setup.exe /r to generate the setup.iss file. Be sure you have the serial number on hand to enter into the setup process. Grab the setup.iss answer file from the %WINDIR% location & place into the folder with Setup.exe. Run Setup.exe /s to install silently.
You should also be able to pass the serial number to the MSI via a property named ISX_SERIALNUMBER. Use a command line simular to:
setup.exe /s /w /v"ISX_SERIALNUMBER= TRANSFORMS=\"<
full path to your transform file>.mst\" /qn"