I've yet to really dig into NaviChord...but having non played notes displayed is really annoying for me, but it does seem to be the convention in tonnetz software for some reason.
Do you play external keyboard and want to see only the notes played externally? Or from the onscreen keyboard?
If there were no circle notes, the only option to play from the grid is by triads, which quickly becomes limiting.
Interesting links, thanks.
There is also Harmony Navigator, a smaller brother of Synfire. I had some good time with it, but it is not very well organized in my opinion.
I've discovered recently SunDog, http://feelyoursound.com/sundog/. Looks interesting from the first sight.