Ok
I have a solution now. I modified the above code to look like this.
var solCurrentConfig = Solution.SolutionBuild.SolutionConfigurations.Add('AutonomousDebug', 'Debug', true);
var currentConfig = proj.Object.Configurations('AutonomousDebug');
debugConfig.CopyTo( currentConfig );
currentConfig = proj.Object.Configurations('AutonomousDebug');
currentConfig.OutputDirectory = '$(SolutionDir)$(Configuration)';
currentConfig.IntermediateDirectory = '$(Configuration)/';