To reproduce:
1) Open the two .bat-files in a text-editor and adjust the pathes for "Unity.exe" and "-projectPath" and save the modified bat-files
2) Execute the .bat-file "BuildLightmap_NoGraphics.bat". After it has finished, open the project and the scene "Scene.unity" in the Unity editor and inspect the lightmap on the two cube-objects. Note that there is no red light bouncing off the ground onto the central cube.
3) For comparison: Close Unity and execute the second bat-file "BuildLightmap_WithGraphics.bat". Open Unity again and inspect the lightmap. Note that now the indirect lighting looks correct with red light illuminating the shadowed area of the central cube.