"Space Seed" certainly muddies up the waters, doesn't it? Consider these scenes:
The first scene aboard the S.S. Botany Bay...
MCCOY: Heartbeat now thirty, dropping fast. It's a heart flutter. He's dying.
MARLA: Do something, Captain!
KIRK: Can we?
SCOTT: It'd take an hour to figure it out.
KIRK: What happens if we get him out of there?
MCCOY: He'll die in seconds if we don't.
(Kirk uses something metal in his hand to break the glass and open the compartment. The man is slid out on a trolley, gasping and awake. He tries to speak.)
KHAN: How long?
KIRK: How long have you been sleeping? Two centuries we estimate. Landing party to Enterprise. Come in.
And consider they are making their first encounter with Khan aboard a drifting sleeper ship with suitably warm breathable atmosphere, lighting and artificial gravity
, (!!!) all of which works after (at least) 200 years.
Later in the "in bed with a knife at your doctor's throat" scene in Sickbay, Khan essentially repeats Kirk's guesstimate and McCoy confirms it. Of course, Kirk's statement was made in a very excited moment, so it wasn't supposed to be taken literally, and McCoy was simply confirming what Kirk said, not the veracity of Kirk's statement.
IIRC, Golstein & Golstein's "Star Trek Space Flight Chronology" from 1980 seemed rotted in the notion that TOS was set in the late 22nd century, so obviously the authors took their cues from the canon dialogue in the series. For quite a while in the late '70's, I subscribed to this view as well. TMP seemed to shatter this house of cards when Decker suggested that Voyager VI "was launched from Earth more than 300 years ago". (That's from my memory... anybody have an exact transcription? I suspect that's the first clear mention in canon that would set TMP in the late 23rd century)
Of course, these kinds of inconsistencies were part of TOS from the beginning. And it's not just the overall, series-wide continuity that had little fractures here and there, it was also fractures within a single script. Consider "Where No Man Has Gone Before":
Captain's log, Star date 1312.4. The impossible has happened. From directly ahead, we're picking up a recorded distress signal, the call letters of a vessel which has been missing for over two centuries. Did another Earth ship once probe out of the galaxy as we intend to do? What happened to it out there? Is this some warning they've left behind?
Note here that Captain Kirk seems to suggest that the Earth ship Valiant "has been missing for over two centuries". But later...
( NOTE: The Chakotyea.net transcript for "Where No Man..." omitted the "almost" in Kirk's intercraft address. )
KELSO: Screen on, sir. Approaching galaxy edge, sir.
KIRK: Neutralize warp, Mister Mitchell. Hold this position.
MITCHELL: Neutraliae warp, sir.
KIRK: Address intercraft.
MITCHELL: Intercraft open.
KIRK: This is the Captain speaking. The object we encountered is a ship's disaster recorder, apparently ejected from the S.S. Valiant almost two hundred years ago...