Although the prototype city was not known to every be produced, it did appear in the Micronaut Marvel comics. Seems the Micronaut artist Michael Golden had access to either the prototype toys themselves or lots of pictures of them. The prototype city was turned into the evil Baron Karza's space-ship as shown in the following panels.
Here Karza is standing on a triangle piece with a hexagon in the foreground from issue #10 of the original run.
Here is a similar pose, with the triangle and two hexagons visible, from issue #9.
And back in issue #7, we see Karza inside the hexagon.
In all cases, Baron Karza's ship seems to be model after the top of th prototype Galatic Command Center.