http://tng.trekcore.com/bluray/okuda3.html
Part 3 of the Oduka's interview is up on TrekCore. They mention in "The Naked Now" that they discuss the TOS Enterprise in the episode but show a diagram of the refit. They've made a diagram of the TOS Enterprise to use in that shot.
I asked Oduka about it on Twitter:
@doubleofive said:
Are you planning on fixing many mistakes like that? You've got to be torn between recreating the original FX & making them better
@MikeOkuda said:
In vast majority of cases, we try to re-create original FX, including artistic decisions with which we disagree.
Not sure why this mistakes warrants fixing when others won't be, but perhaps it was because it was his mistake to begin with, though they're keeping the graphics green even though Oduka wanted them white.
I don't mind fixing little mistakes like this, I guess, but I'm worried because TOSR started as a shot-by-shot enhancement of effects that turned into a bit much at times.