If you think about it, it actually kind of makes sense. Unlike most of us here on MacRumours where we know about the features of the iPhone/iOS, you have to remember majority, or at least a good percentage of the market that buy iPhones/iDevices/iWhateveryouhave aren't that technological. There may be people that don't know FaceTime even exist, so Apple is making it more known, with the addition of its own icon.
Apple made it its own app because according to some consumers they couldn't find FaceTime, and on iPod touch and iPad it is right there, (even though these devices lack the Phone.app)