I'm afraid this isn't the best choice of material for a pipe/digital organ comparison. In each example only a few flute stops are pulled, and these are largely masked by the orchestral strings. A solo organ recording of a large instrument with all the stops drawn would be a much better example, but even then I doubt anybody would be able to tell the difference between a pipe organ and a well designed and implemented digital/electonic instrument.
When Allen first introduced the digital electronic organ in the 1970's the difference between a pipe organ and a comparable size Allen digital organ was immediately obvious, even if only a few stops were pulled. Listening to the pipe organ one would hear several completely independent windblown pipes sounding, each slightly out of phase with the others, each having its own characteristic attack sound (the "ch" sound organbuilders call chiff), its own randomly variable continuous sound caused by random changes in the wind mechanism, and its own decay sound. With the Allen, when a key was depressed all the stops that were drawn started their sound with a unified thud, followed by a monotonous unvarying sustained tone, and ending with a guillotine-quick silence when the key was released. To add insult to injury, as additional stops were drawn all the sounds eminated from a single dac and were fed through one amp to one speaker, resulting in an increasing level of im distortion that caused the organ to sound synthetic and opaque. Anybody with a small SET amp can imitate this sound by playing a recording of a full organ and turning up the volume until the sound becomes heavily distorted.
Today's better digital organs are very different. Typically, a separate dac is used to originate the sound for every one or two stops. This sound is then fed through a separate amp and speaker system, causing minimal im distortion. Today's organ dacs are more sophisticated, producing an accurate attack, sustained tone, random variations, wind sound, and decay. I recently attended an organ recital on a new Rodgers three manual organ, and if I hadn't known it was a digital organ I would have assumed it was a pipe organ with the pipes hidden behind a screen.
Here are a few examples to demonstrate the differences:
First, the worst of the worst, a Bach Toccata performend on a pre-digital Hammond organ:
http://www.youtube.com/watch?v=3PiNecvAws4Second, a small budget priced analog (pre-digital) organ. Notice the individual stop combinations don't sound very convincing, and toward the end as more stops are drawn it begins to sound even more like an electronic organ:
http://www.youtube.com/watch?v=xioxm8CnJPgA small contemporary digital organ. Notice the individual stops sound reasonably convincing compared to the previous examples and the full organ toward the end doesn't sound too congested, but it still doesn't sound like a pipe organ:
http://www.youtube.com/watch?v=17ObLhCaHyAExample of a larger Rodgers digital instrument that I could easily mistake for a pipe organ:
http://www.youtube.com/watch?v=wnGLjKv1MSoExample of a large pipe organ:
http://www.youtube.com/watch?v=_FXoyr_FyFwAnd finally, the master of 20th century stylized hymn playing, Virgil Fox, accompanying the congregation on the very large pipe organ at the Riverside church in NYC. Not a good recording, but you'll still feel the majesty of this famous instrument:
http://www.youtube.com/watch?v=JSbNgX1_-SA&feature=related