How to add custom 3d packages path to pcbnew
You can add your own variable in the Preferences->Configure Paths...
You might need to restart KiCad for the variable to be seen by other KiCad editors.



Then edit your footprint module and in 3D Settings add your custom wrl. Once added the absolute path will be replaced with the above defined path variable.



I'm running KiCad v5.0.0.