Here is the relevant code inside of CreatePakResponseFileFromStagingManifest for my explanation below.
Right before the exception, CreatePakResponseFileFromStagingManifest inside of CopyBuildToStagingDirectory.Automation.cs converts BOTH of the paths <ProjectDirectory>\\Engine\\Config\\DefaultEngine.ini and <ProjectDirectory>\\<ProjectName>\\Config\\DefaultEngine.ini to <ProjectDirectory>\\<ProjectName>\\Saved\\Temp\\Win64\\DefaultEngine.ini
Since this code sets the Src to the same value, but with different Dest values, it triggers the AutomationException.
I’m not sure why this would be happening now, as this project has always been structured this way.