The following command line options are supported by the Setup Factory installer:

/S:<<optional ini file>>

Allow an install to be run in silent mode. As a result, no screens or dialogs will be shown. If /S is passed on the command line it will set the global variable _SilentInstall to true if the Enable silent/unattended install option is selected in project settings.
This command line option also has an optional INI file that can be passed containing session variable values. For example:
 
"C:\output\setup.exe" "/S:C:\setupvars.ini"
This will cause the session variables in the INI file to be used for the setup. The INI file should be in the format:
[SetupValues]
%AppFolder%=C:\Program Files\Your Product 2
%UserName%=Joe Blow
%Whatever%=Who knows

Every setup executable requires some temporary space on the user's hard drive during the installation process. By default, Setup Factory uses the user's TEMP directory for extracting temporary files and other miscellaneous operations. You can force the setup executable to use an alternate directory by using the /T command line option.
The syntax for the /T option is:
/T:<<file path>>
Replace "<<file path>>" with the path to the folder you want the setup executable to use for its temporary files. (Be sure to put quotes around the entire argument if the path includes any spaces.) If the folder doesn't already exist on the user's system, it will be created automatically.
For example:
 "C:\Downloads\setup.exe" "/T:C:\My Temp Dir"
(forces the installer to use "C:\My Temp Dir" for temporary files)

This command line option hides the "initializing..." dialog that appears when extracting dependency or primer files at the beginning of the install.

This command line option forces the Setup Factory launcher of a multi-segment install to wait for the setup executable to return before exiting. This is useful if you're running the installer from another process and you want that process to wait for Setup Factory to finish before proceeding.
Note: This only applies to muti-segment setups since Web (Single File) setups always wait for return.
Note: It is best not to use the /W option on very large multi-segment installs because errors may occur due to memory issues. If the /W command line option is not used, the setup return code will always be 0 since it is being returned after the launcher performs the initial extraction.

Uninstall Switches:

The following command line options are supported by the Setup Factory uninstall program:

/S:<<optional ini file>>

Allow an uninstall to be run in silent mode. As a result, no screens or dialogs will be shown. If /S is passed on the command line it will set the global variable _SilentInstall to true if the Allow silent uninstall option is selected in uninstall settings.
This command line option also has an optional INI file that can be passed containing session variable values. For example:
Note: The /U command line option also must be used when calling the uninstall program. See /U for details.
"C:\Program Files\MyProduct\uninstall.exe" "/U:C:\Program Files\MyProduct\Uninstall\MyProduct.xml" "/S:C:\setupvars.ini"
This will cause the session variables in the INI file to be used for the uninstall. The INI file should be in the format:
[UninstallValues]
%UserName%=Joe Blow
%Whatever%=Who knows
 

This command line option must be used when calling the uninstall program from the command line. The location and filenames of the uninstall executable and configuration file are defined in the Uninstall Settings. For example:
 
"C:\Program Files\MyProduct\uninstall.exe" "/U:C:\Program Files\MyProduct\Uninstall\uninstall.xml"

Source is Indigo's guides: http://www.indigorose.com/webhelp/suf9/index.htm
More information can be found in the above link, including build switches and exit codes.

Hope this can help someone else.

Cheers