You still need to update the library tables if you set personal path variables. (After all the library tables are what matters. Path variables just make the library tables portable.)
So either delete the original lib table entries using the default kicad path variables and replace them with your own. Or point the kicad default path variables to your personal repo locations.
For 3d models you are kind of forced into the latter route anyways as footprints use the KISYS3DMOD path variable for pointing to 3d models.