Making this decision known only to the licensees covers his ass legally, since the licensees are the part of the publicity machine that he'd have the least control over; everything else, like script submissions, can be booted with the cover excuse of how they don't want to see retreads of previous stories this soon, without having to cite TAS' "off limits" status directly.
GR was supposedly
extremely concerned that the licensed tie-ins were contributing to a dilution of what was, in 1989, a much bigger juggernaut than it had been. He detested the flier he saw, where Diane Duane was called "the creator of the Rihannsu". He was dismayed when Gerrold and Fontana pressed to be credited as co-creators of TNG, and therefore I can imagine that shunting TAS into the realm of non canonicity was a convenient way to diminish their ST contributions. The renegotiation of licenses in 1989 allowed GR to be contractually specific about what elements should be featured or not featured in the tie-ins. Richard Arnold used to say the new focus of tie-ins, from 1989, had to be on "the big seven" characters of TOS and "the big eight" of TNG.
It really wasn't a case of
not telling the public that TAS was now off-limits. It wasn't really their business. In any case, DC Comics did publish a quote from "the memo" to explain why Arex and M'Ress had gone, and one of the ST novelists had put the text of the memo sent to licensees up onto GEnie and Usenet. Richard Arnold enthusiastically regaled convention audiences that "the animated characters don't cross over with the movies" if some hapless comics fan enquired about the renewed license contracts of 1989.
But don't forget, this period wasn't the first time that the likenesses of Arex and M'Ress had caused difficulties. Two (uncredited) Alan Dean Foster storylines were turned into comics for Power Records. He thought he was only supplying scripts for audio productions.
Arex was redrawn, at seemingly the last minute, as a blond caucasian male crewman, Mr Connors, who just so happened to have a huge Edoan musical intrument in his cabin that he dragged up onto the bridge. You can see the paste-up changes where "Arex" become "Connors", and weird gaps that seem to suggest a missing leg.
("The Crier in Emptiness"). In the accompanying comic, M'Ress was redrawn as a bluish hominid woman, vaguely resembling Marta the Orion, but still called M'Ress the Caitian
("Passage to Moauv").
This incident is a good indication that the Filmation contracts put the likenesses of Arex and M'Ress under a legal cloud long before 1989, and that when DC Comics added them to the comics cast, no one had realised there were contractual restraints or permissions required.