The recording of the Content is derived from the line output connections on the organ, and so has no room sound, just the reverb on the organ. That's probably why it sounds closer. Also, the samples Content use, although good, aren't on a par with the best (not surprising given the price of the Content). It does the job pretty well though.
The pipe organ was recorded using the stereo mics on the camcorder (a Sony model that's really a digital audio recorder with a very basic HD video camera attached. Position was a compromise between being reasonably close for the picture, yet far enough away to try & pick up both sides of the organ (and to try & avoid getting too much "chatter" from the others in the meeting!)