I had read that they did not add that clause, which is pretty common, ask Natalie Portman regarding doing Thor 2. But I could be wrong.
I believe that you are incorrect. I got this story from Bjo Trimble, who met Kirstie Alley at a Star Trek convention between STs II and III, and Richard Arnold used to relate the same story at conventions in the late 80s and early 90s.
And, if there was no clause in Alley's contract, Paramount would not have had to even bother with making an offer.
Don't forget that, as with Decker, Ilia and Xon being the new crewmembers who would carry "Star Trek: Phase II" if/when Shatner dropped out after 13 episodes, Saavik and David were thought of as characters who could carry a series of Spockless telemovies if/when Shatner's regular movie career took off, as he'd hoped.
To groom an actress as a potential longterm Spock replacement and not include the right clauses in her contract would be highly unusual. "Thor 2" could easily survive without Natalie Portman. Star Trek telemovies needed a Vulcan placeholder for Spock.
Catrall, who was Meyer's second choice to fill the role in TUC...
More importantly, Cattrall was Nick Meyer's personal first choice for Saavik for ST II.
After all Shatner's relationship with most of his regular cast mates off screen is well known to be the opposite to the on-screen.
It is now, but not that widely known in those early days. The long-felt bitterness emerged when all the cast were writing their autobiographies.