I suspect you'll find that iTerm2 is not unusual in this respect. The reason is that we only modify that file through a system API (NSUserDefaults is the class). I didn't know you could create symlinks to dropbox; I was thinking about how we could move prefs into DB so they could be shared between machines.
I would like to make this work. I think the solution will probably not involve a symlink, and will require setting a file in Preferences. Please file a bug for it and I'll look into it.
Thanks,
G