I think the idea isn't to refit the entire ship (which happens in the first movie) but to test the engine design which eventually comes in that first movie. The ship is basically the same... but the engines have been swapped out with the new design. And, if you look at the Phase II concepts prior to the movie, the ship was more or less externally the same with some modifications, the most modification being to the nacelles.
It's an interesting direction to take New Voyages/Phase II and yet really has nothing to do with the characters, per se. Also, pretty ship with or without the different nacelles. :-)