I checked that both apps (pre-installed and paid) have different version numbers.
MacOS – What’s the difference of FaceTime App that came installed in the Retina Macbook Pro and the one that is in Mac App Store for $0.99
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Best Answer
FaceTime in the App Store is really only meant for users of 10.6 Snow Leopard. As of 10.7 Lion, FaceTime comes pre-installed.
I'm not sure why Apple was charging for FaceTime in the first place. Perhaps just testing the Apple Store sales model.