Makes more sense than "Mawdryn Undead"'s misreading of the UNIT timeframe. "The Web of Fear" said that 1935 was "over forty years ago," putting Lethbridge-Stewart's debut appearance in at least 1976, and "The Invasion" was 4 years after that, so at least 1980. And yet "Mawdryn" said the Brig retired in 1977! (And, yes, "The Pyramids of Mars" had Sarah Jane say she was from 1980, so there was an issue there too.)
The difference with some of these issues is that they were created in order to tell the story at hand.
"The Two Doctors" seemed to be relying on the fact that, at the time, very few people would have remembered the status quo from 16 years earlier. There had been almost no reruns of the Patrick Troughton years up to that point and the precious few VHS releases had all been of Tom Baker stories. (Troughton's first VHS release, "The Seeds of Death," was released approximately 4 months after "The Two Doctors" aired.)
In the case of the UNIT dating in "Maydryn Undead," it's simply a matter of the writers not doing their homework. They assumed that the UNIT stories took place in the present, not 5-10 years in the future. (And that's assuming that the slightly addled, distracted Professor Travers gave the right time frame when he said "over 40 years ago" in "The Web of Fear." I'm not sure how well I'd trust him with specifics like that.)
That's a very different thing than concocting a line out of thin air about Ian & Barbara not aging, with no on-screen explanation or even vague indication as to how that happened!
Unless you buy into Terence Dicks's "Series 6B" theory that the Second Doctor did go on missions for the Time Lords after the trail in The War Games but before regenerating, even to the point that the Time Lords eventually allowed Jamie and Victoria to work with him. It was first introduced as a way to keep Doctor Who comic strips running while waiting for Pertwee's episodes to air, and has since been the basis for a few novels, usually written by Dicks. The Second Doctor's appearances in The Three Doctors and The Five Doctors also take place during "6B" from his perspective, thus explaining how he knows about Jamie and Zoe's fates in The War Games in The Five Doctors.
It certainly explains him knowing about Jamie & Zoe in "The Five Doctors."
Meanwhile, in the novel "World Game," which seems to immediately lead into "The Two Doctors," it seems to indicate that Victoria never actually worked with the Doctor in Season 6B. It's just that, from Jamie's perspective, based on how the Time Lords have doctored his memories, this is right after they parted ways with Victoria.
As for "The Three Doctors," I don't think there's anything definitive about when this takes place during the 2nd Doctor's timeline. It would certainly make sense for it to take place during Season 6B. That would probably make it easier for the Time Lords to track him down at that point. But since "The Three Doctors" doesn't contain the same kind of glaring continuity errors as "The Five Doctors" & "The Two Doctors," there's a lot more freedom to place "The Three Doctors" anywhere you want so long as it's after "The Invasion." (He does remember fighting the Cybermen with the Brigadier and meeting Benton.)
In the first season, in "The Aztecs," they insisted that history could never be changed, "not one line," and then a year later in "The Time Meddler" they were trying to stop the Meddling Monk from changing history.
In "The Aztecs," I interpreted that as the Doctor telling her that she
must not change history, not that she
could not if she tried. After all, if history can't be changed, if it's all a big predestination paradox, why bother arguing the point with Barbara?