The thing I am getting at is that "retcon" means "retroactive continuity." It doesn't matter what Khan says during TWOK about what happened in "Space Seed" -- if we didn't see it on screen and none of the characters say or otherwise indicate that it happened -- it didn't happen. Hence, retcon.
I know what a retcon is.
Your interpretation of retcon is more severe than we are used to seeing and using. For me, a retcon infers that we are supposed to forget a previous canonical factoid because it's just been overridden by a new canonical factoid. But TOS never said that Chekov wasn't on the ship during "Space Seed", so ST II didn't overwrite such a statement.