Any RTMP family protocol (including RTMFP) can be used for connection between FMS & Flash Player (last hop connectivity). Connection between FMG & FMS is always RTMP, since FMG always uses RTMP. However, that is not expected to have significance in most deployements.
But now I have another question:) How many connections between FMS and FMG? One per each flashplayer connected to FMS, or there is some kind of sharing?