In classic Daggerfall, the ghosts are transparent. In Daggerfall Unity, the standard shader will make the ghost opaque like any other enemy by default. I used an XML file for the ghosts and wraiths to override the standard shader to use the "fade" shader variant instead. Unfortunately, although it looks correct inside the Unity editor, it doesn't work correctly inside DFU because the fade shader variant is getting culled from the DFU build.
TheLacus is going to add this shader variant into the DFU core game to resolve this issue.
Edit: The issue has been resolved in the DFU core and will be integrated in to the next release of DFU.
Just out of curiosity, why are using a graphics upscaling mod in tandem with Retro mode?