Exactly.
When was general order 7 instituted?
In 2161, when the UFP Starfleet was organized. It's just that the death penalty clause inherent in all General Orders was activated for GO7 on the specific case of Talos IV some time after Pike and Spock chose to recommend it. Thus probably a bit after DIS "If Memory Serves".
And then it was deactivated, when it became evident it didn't serve its purpose. And then it was activated on GO4, the nature of which is not known (save for it having nothing to do with mutinies). And then no doubt again deactivated there but activated on GO 13, when the next starship captain stumbled onto another galaxy-shattering crisis that called for extreme deterrent.
Another pertinent piece of info is that, on Starbase 11, Mendez said that the Enterprise was the only "Earth ship" ever to visit Talos IV. Trying to split the hair and claim that in that context Earth ship doesn't mean Federation ship isn't going to fly.
We can decide that all other missions were censored out of existence, and we can decide it happened in the same process that saw the death penalty clause activated. That is, it had already been several years since "The Cage", so it was way too late to pretend this one did not happen - but the cloak and dagger machinery would go full throttle on the incident where the
Discovery and a S31 intel cutter visited, as well as on all later incidents.
Interestingly, and even without DIS input, this also means the
SS Columbia never existed. Which only makes sense. Everything in "The Cage" from the teaser on has the heroes within the clutches of the Talosians: the SOS they sail through is an illusion, as evidenced by it instantly transforming into one establishing survivors when the heroes decide this is what they require in order to act. So any records referring to the existence of the
Columbia are illusions as well.
So, in "The Menagerie," the switch to illusion-Mendez probably happened right before he boarded the shuttlecraft with Kirk.
The Talosians were messing with our heroes before the teaser already - otherwise Kirk would have learned of Pike's predicament months prior, when the rest of the galaxy was discussing it. Might be there never
was any Commodore Mendez, and the
Enterprise never visited SB11 where Commodore Stone kept on doing his good work.
Apart from that, we can remove a Mendez and substitute another at any point of the adventure - the Talosians are that good at what they do. That Mendez would absolve our heroes in the end is probably the most dubious bit of them all. After all, he should be dead: him listening in on what happened means he, too, is guilty as sin, and would have been lax in his duties if not organizing an execution squad for himself.
Timo Saloniemi