Since you see setup.ini I assume you also see setup.exe and the MSI file. Just skip right over the setup.exe all together and use:
msiexec /ifoo.msi /qn
The only reason you need setup.exe is if you are counting on it doing things like installing MSI Runtime, .NET Framework, Setup Prereqs or IScript engine.
As for UNC ignoring setup.ini, I've never seen that one before. I run my setup.exe's from UNC paths all the time without problems.