^Yes, but the familiar "Space Seed" shots are just still photographs documenting the shot setup on the bluescreen stage. They aren't the actual footage that would've been shot by the FX camera itself. The way it works (or worked, rather) is that the scene is shot through a red filter that blocks out the blue light, so that what ends up on the film is a shot of the ship surrounded by blackness -- or, on the negative, by clear film. (And that's then processed to create the inverse matte, a silhouette of the ship which is used to burn a ship-shaped "hole" into the starscape footage so that the two can then be combined without the stars showing through the ship.) If this were a frame from the actual film shot by the FX camera, then the blue light would've been filtered out and you would've gotten an image of the ship against blackness.
And if it were that raw FX footage, then it would've been shot through a red filter which might've changed the color of the ship (which would've been color-corrected in processing). The overall red tinge of the deteriorated film may have obscured that.
Often the bluescreen was only part of the matting process; black sheets or partly blacked-out plates of glass, called "garbage mattes," would be positioned in front of the camera to block out the stand that supported the miniature or any other equipment or stagehands that would otherwise get in the shot. It's possible that what we're seeing here is the result of a misaligned garbage matte that blocked out most of the ship instead of just the stand.
Although I can see two problems with that proposition. One, the photos we have suggest that the miniature stand was painted blue, not blocked by a garbage matte. Two, the red filter isn't always perfect so there can be a difference in the quality of blackness between the bluescreen area and the garbage-matte area. (In the original FX footage of
The Empire Strikes Back, this difference produced visible angular "blobs" around the matted miniatures, which were nearly invisible on the big screen but quite blatant on television.) So your photo-lab person could've probably detected that difference.
Anyway, I checked out
Star Trek History and it shows some test shots the Howard Anderson Company did of the miniature in 1964, which do seem to have been shot against a black background (although some of the shots there look like the background has been mostly painted out by the restorer, so I can't be certain). So this could come from those test shots. Maybe they were specifically doing a lighting test on the nacelles and didn't bother to illuminate the whole ship?