That thing about the gift of a polished stone is the smoking gun. INSIDE STAR TREK (Justman, Solow) talks about Gene's first wife having the hobby of polishing stones and mounting them as costume jewelry.
Just because I found it at the moment, the passage in question is on page 73 of the book. It indicates that polishing stones was a hobby of both Eileen and Gene Roddenberry.
I've seen Ellison in person twice, and he's struck me as a straight-shooter. Considering the fact that Ellison was always protective of his work -- he used the Cordwainer Bird pseudonym on a number of television episodes he was dissatisfied with -- the use of his real name on Star Trek
is a bit odd, especially since he was vocally dissatisfied with the final episode.
In light of that, his is the only explanation that makes sense.