Okay, so I found the fix to this issue. You have to clone the 'Surfliner' folder inside of Assets\RSC\PacificSurfliner\RailVehicles\Passenger\. If you don't do this, the GeoPcDx will keep referring to the 'Baggage' folder in the 'Surfliner' folder.
A picture is shown below. The left is a car without the logo, and the right is a car with the original files.
