Interesting to note that one of the neck windows is orange on the decal sheet for the Polar Lights 1/1000 scale TOS kit. The exact same window on the other side is orange, also.
If I'm not mistaken, I recall seeing a close-up shot of the neck (can't remember what TOS episode it was) and that same window was lit up orange on the studio model. A marker light perhaps, instead of a window? Only Tom Sasser would know the answer to that since he designed the kit.