Are you sure this wasn't just a piece that would be cut out in order to mount a light?
It wouldn't press against the dome, it would be covered by it. The dome wasn't going to be a flat piece like with the TOS model (shown on the prints) but a concave thingie (yes, that's the technical term, thingie, dammit!) It was supposed to be a more sophisiticated lighting setup for the ship than what had been done up until that point.
The refit nav deflector is concave
, the dome over the bridge is convex
I can't speak to the "insets" you said you saw on a photo. All the photos I've seen of the model are at a stage where the bridge dome appears to just be the solid casting we see in the photos with a half-donut indentation in the top, as seen on the left photo in the image linked below.
The plans show a shallow TOS type dome that would--at the scale of the model--would have cleared the nub by maybe 1/4 inch. Or are you saying and array of lights would have set in the concave bundt-cake pan?