Gavin, you can use any ND linear grad filter which has marks on the outer ring, i.e. Heliopan filters. Or you can use the Cokin system, which allows you to shift the filter up and down.
The autofocus is not TTL, it's based on a triangulation system similar to the Zeiss Ikon or Leica, but in auto mode, so it does not interfere with any filter.
Though I use circular pol filters for my other cams, I don't use any filter on the Contax G system because the Zeiss lenses are the best I've ever seen for 35mm cameras when shooting slide film.