Is this going to change?
Enterprise 8.8 patch 3 for Windows 8 uses Setup_Win8.ini and Setupvse_win8.exe and VSE880_Win8.msi but MID only applies changes to Setup.ini, Setupvse.exe and VSE880.msi (as far as I can tell) so even if you use the patch files option in MID any other settings aren't applied when installing on Windows 8.
It would be good to be able to use Installation Designer to create a configured installation package for Windows 8
We expect MID to be usable again for customizing packages that will install on any supported operating system in the Patch 4 release.
There is no MID-workaround for Patch 3 installations.
However, if you have a configuration file already (the vsecfg.cab, can take it from any VSE 8.8 installation you have which was customized) then perhaps you do have a workaround. Drop that file into the \MID subfolder on your Windows 8 installation of VSE.