I don't have a low-level explanation, but I know that is the limitation: You need vp6 or Spark video, and RTMP player, for full trick player features with Wowza.
You might be able to do trick play in a Silverlight player (smooth streaming) or OSMF player (sanjose/HDS streaming). There are trick play features in the Silverlight smooth streaming API, though they didn't work for me when I was working with that a couple of years ago, and we don't have any examples.
For HTTP streaming clients, trick play is all done in the client, if it is supported; Wowza is not involved except to deliver the chunks. For RTMP playback clients streaming VP6 or Spark video, Wowza is involved in trick play. FFmpeg or GStreamer are sources, and not involved in trick play in either case.