He's probably referring to Ellison's book about writing the script, that included the script and a couple of treatments, along with the first act of someone else's rewrite that he passed off as his own.
The script itself is, for a teleplay, an extremely well written short story. It is compelling, it has a plethora of well developed characters, and has consequence. But it isn't Star Trek. Ellison used the toys of Star Trek to tell his own story, and, in my opinion, attempted to rewrite Star Trek into something far different than the hopeful look at the future that GR had intended, which falls directly into Ellison's particular take on humanity.
Included in the book is an essay that Ellison had been putting together for a long time, and was obviously intended to not see the light of day until GR was long dead. This essay, a screed against GR and everything he represented, even against Star Trek itself, puts a particular spin on the events surrounding the writing, and ultimately rewriting, of the script for COTEoF. I'll leave it at that, as I know too many people that believe every word, even when they know better from personal experience.
Edited to add: I just read Paul's post above, and I realize he's referring to the IDW miniseries that serialized the teaser and each act in five issues, and was then combined into a trade. This was just a couple of years ago. I only read the teaser, but it followed the original pretty much exactly, if padded visually to take up the page count. I didn't like their character design for Beckwith, as it didn't look like Ellison's description of him.