You may call the original painting a "myth" but I was there when it was originally unveiled at the Smithsonian in (I think) 1976 and studied it extensively. To me it appeared freshly painted and I believe one or more of the windows were painted over. Believe what you want but the color that was used to repaint it did not even match the original color; it was slightly more blue as compared to the more greenish original color.
If you compare photos from that time that have both the top of the saucer and the rest of the ship it seems pretty obvious that it was repainted (a different color no less). Compare the rim of the saucer with the top of it in the below photos; the top is a different color. Make your own judgement but I know what the evidence tells me. Also, when the miniature was uncrated; there were numerous sheets of replacement decals that could have been easily applied to replace the originals after the painting. Again, believe what you want but I see people so dogmatic in what they believe that they are not open to any other options.
The Smithsonian website says:
"Over time, heat, cold, humidity and other elements had taken a toll on the structure, the wiring and other internal components as well as the exterior paint scheme. Before it could be put on exhibit, extensive restoration was required. The first Smithsonian restoration took place shortly after the starship was received and was completed by July 29, 1974."
Extensive restoration, damage to the structure, wiring, internal components and exterior paint scheme sounds like it was more than touch-up on the exterior paint. Apparently it is (or was at the time) the policy of the Smithsonian to leave at least a portion of the original vehicle untouched and in this case it is the top of the saucer. Draw your own conclusions but I know what I saw then and the color difference in the photos seem to bear that out.