The one aspect of his original design he seemed to not want to let go of was how far apart the nacelles were from each other... either he didn't know that they were moved closer together on both models or he didn't care for the fact that they were moved together.
I personally think they look better closer together.
Speculation on my part but how far out of true would the measurements be if the nacelles were only supporting themselves? IOW, would they torque at all under the pull of gravity? Toe in at the caps and toe out on the aft ends? Enough to account for a disparity in measurements? Especially if you were having someone re-measure the ship for you...
Just a random thought I had reading your post.