For War Horse, it almost seems like Williams recorded multiple takes of many cues, and the music editors went off and chose the ones to use for the film and WIlliams went off and chose the ones to use for the album without the two parties concerning themselves with what the other used.
I think it's the other way around (Williams chose the takes for the film and the music editors the ones for the album), but I guess Williams had a word for the OST as well. However, in the official EPK interview Williams clearly says that the performance for this score was something quite important to get exactly right. I guess there are a lot of alternates lying around on the cutting room floor
On a sidenote, I think it's possibile to create an expanded edit of the score using both the OST and the FYC, but it's a job that requires time to study and analyze carefully both CDs before attempting at it.
Also, did someone else noticed that the FYC sounds a tad better than the OST? I listened to it only once, but it seems there's less artificial reverb added and a dryer, leaner sound which seems more natural.