You must be mistaken. The CBS Digital Enterprise is proportioned as essentially an exact match for the physical 11-footer. When you see proportions that look different, it's a matter of camera angle and what type of (real or digital) lens was being used. Lenses make a huge difference, and TOS original fx used them brilliantly.
These are the only differences between the ships that might stand out to a casual viewer:
- The 11-footer's lower saucer came of of the mold imperfectly in 1964 and is slightly out of round. The CBS Digital model corrects that to perfectly circular.
- The CBS ship has no risk of misaligned nacelles, a difficult feat for such a large practical model to achieve all the time.
- The CBS ship (2nd, refined version) adds a window to complete the broken row of windows on the forward side of the lower saucer. The digital ship has seven windows in a row, all lit, instead of six with a gap, two of which are dark. I personally disapprove of this change a lot; the original looked more real (internal structures mean you can't put a window everywhere).
- The CBS Digital ship uses the wrong font for "U.S.S. Enterprise NCC-1701" on the upper saucer.
- The CBS Digital ship appears to be a darker gray, but most of this difference is due to more "realistic" lighting choices. Also, the main deflector dish is a metallic copper color on the original, and somewhat grayish on the CBS version.
- The CBS ship's upper saucer has all four square panels lit, while the 11-footer had lighting in three of them, while the portside aft panel was just painted on the saucer.
I'm sure there are other differences in the detailing, but again, the CBS overall proportions are right.
Also another improvement that the CGI managed to do was the pearlescent paint scheme. Apparently the original model was painted in pearlescent paint to make it glow or just stand out, but it also caused problems with the green screen, as it would reflect the green cloth, which is why a couple of shots either had a torpedoe hole through the saucer or nacelles floating above the engineering section with no pylons attached.
But you should also remember that with the original effects we are also seeing generational loss". Even when the original 40-volume DVD set came out, I couldn't help but notice that in some of the later episodes, most likely because the reprinted the completed effects, the Enterprise appeared white, with no hint of grey, and even the smaller details, like the red lines on the nacelles, were either partially or completely missing.