It depends. First of all, the only way (AFAIK) that the media player notes that a file is played is by setting its playcount, and this only happens when you play it fully (or at least to some percentage of the full track). Second, we could create another "daemon" that watches in the background and watches D-Bus for "play" events from MAFW (the backend for the media player). I guess you don't want to have gPodder itself running in the background while you are operating with media player, right?

Another (likely) option is that Panucci does take care of the play position and playcount (which it already does to a degree) and Panucci and gPodder will handle the "played" status of the episodes together, so when you play something in Panucci, gPodder will notice the next time it starts.