Yea, has to be run in the same site and domain as the schema master.
You dont need to move the schema master though. Just run the prep commands from a server in that site and domain. You can download the binaries and run from the command line
You may need to upgrade .net on this server etc...
Sample:
E:\Setup.exe /IAcceptExchangeServerLicenseTerms_DiagnosticDataON /PrepareSchema