Facebook seemed to penalize(not as much exposure in fan's news feeds) the posts that were made to Fan pages through 3rd party apps, as opposed to posting a web link directly to the Fan page itself.
With regards to this, the official Facebook app acts in more or less the same way as SFC does in publishing, although they use a different method. However, posts made by it still show up as from the "third-party" app (which isn't really "third-party", since you have to make the app yourself.. it's your app, you're not a third-party. :)
I've never been able to see any significant difference that could be counted as "penalization" when you make your own app and are the only one thereby using it. The main penalty I've seen discussed is when you're using somebody else's generic app to publish, which neither this nor SFC would do.