I just checked the shots on Trekcore; all four shots of the B in the Nexus were done with the digital model.
http://movies.trekcore.com/gallery/albums/generationshd/generationshd0192.jpg
http://movies.trekcore.com/gallery/albums/generationshd/generationshd0219.jpg
http://movies.trekcore.com/gallery/albums/generationshd/generationshd0288.jpg
http://movies.trekcore.com/gallery/albums/generationshd/generationshd0292.jpg
Looks like the real model to me. What tells you that it's the CG model?
From what I've read, they used the digital model for an additional lighting pass which they composited on top of the footage of the miniature. So everytime a CG energy lightning bolt thing gets close to the ship, it casts the light properly.