This is because the "Program Path" in TFE is set from the cwd on startup. However for mods that's not a sensible location ,as they want to live in $XDG_DATA_HOME. A patch should be added to hardcode the mod path to $XDG_DATA_HOME/Mods, and possibly one to make sure the Program Path is /app/bin as other parts of TFE may expect this to point at the main executable's directory.