No idea offhand, but when I do a scripted installation I use msiexec.exe to run it. That's how you usually automate Windows Installer. See http://support.microsoft.com/kb/227091
for a list of msiexec command line switches.
I usually don't use the installer from Visual Studio to build most of my installation packages, I usually use InstallShield for that. With InstallShield I end up with one setup.exe package that includes the addin.msi file. So I don't end up with separate setup.exe and addin.msi files. You can see if setup.exe can be automated using msiexec, if not you can always automate the msi file that's also generated. I believe that eliminates a number of the bootstrap checks done by setup.exe, so that may not work for you.