The grids used in ReFRESCO can and usually contain polygonal cells, for example when they have been created with Hexpress or other non-structured grid generation packages. The code itself is fully unstructured, face-based vof.
Apart from ParaView, we also use other visualization packages that read CGNS (e.g. Tecplot) and we will not move to the new NGON/NFACE formulation before all the tools support that. For the users of ReFRESCO it would be very inconvenient if they need to convert their results from the old format to the new format only for ParaView, and also keep the old format for other tools. That would mean that they need to convert and keep both files, which takes time and storage.
I would like to make a case for having backwards compatibility in the ParaView CGNS reader, mainly from a usability, convenience and storage perspective. I think it would hurt the willingness to adopt ParaView for visualization, while we are currently seeing a greater and greater adoption of ParaView by our users. Furthermore I think it is expected from a tool like ParaView to have backwards compatibility - I would be very surprised if Tecplot would drop compatibility for the old NGON/NFACE format.