I'm not I'd qualify TOS as "highly" episode though, since some episodes have direct continuity or refer back to earlier ones, especially at the series went onApparently you are ignoring the concept that in a highly episodic television series one can assume that most of the episodes - all of the episodes except those which are clearly sequels to earlier episodes - happen in separate alternate universes, different from the alternate universes of all other episodes.
Since TOS and some other Star Trek series are highly episodic, this concept may apply to them.
So if "The Conscience of the King" and "The Galileo Seven" happen in alternate universes, Kirk may not be traveling to planet Benecia any time near the time of "The Galileo Seven". In the alternate universe of "The Galileo Seven" Kirk may encounter the Karidian Company at an earlier or later date or maybe not at all. And in the alternate universe of "The Conscience of the King" Commissioner Ferris may need to get other transportation to the take the medicines where they are needed, and mayor may not find that transportation in time to fight the plague.