Black box models aren't anything new; in CE3K they shot a real tollgate, then, in order to get the saucers to fly through them, Jein built black metal boxes that lined up with the real tollgates, then flew the saucers through them on poles and laid that in over the live-action. Of course, that was a lock-off shot, but since Abel and Taylor were ambitious, it would make sense to try to 'up the ante' on TREK. Plus, Trumbull talks about being able to 'scale' camera moves on CE3K, by just dialing in the difference between models and live-action. THAT sounds like what would have been needed on TREK, so again, maybe they were doing hardware/software stuff so that the E&S previs could be ported from mo-con setup to mo-con setup, with 'scaling' already built into the camera directions.
That trench shot in the cards was the one card I had for awhile. A friend had the set, and I got him to let me have that one when he moved. Looked much better than the test on the dvd.