From what I've read, as the movie series went along, Roddenberry spent less and less time dictating memos of any sort about them. In the Star Trek II production files there are a number of detailed memos from Roddenberry about the script; in the Star Trek VI production files there are none.
Indeed, on that last film, Roddenberry elected not to take his usual "executive consultant" credit -- although he still took the money.
Interesting. I may just not be remembering what Shatner said. What I do know is that it was never confirmed that Gene was the source of the memos. But both Shatner and Nimoy suspected he was behind it. Bennett tried to smooth things over by including as many of Roddenberry's small ideas as possible in the films to appease him.
Another interesting thread from Shatner's book is the saga of David Gautreaux (Xon). Majel Barrett tried to get him removed from Phase II
by bringing in a British actor who turned out to be terrible at his script reading. Then he was left hanging once Wise started trying to recruit Nimoy into the picture because TPTB realized Xon was unnecessary if Spock returned.