Indeed, why should we treat Trek's 1996 differently from its 2063? I for one intend to still be around to witness the total failure of the Vulcans to arrive.
There are things stated about Khan and his ship and travels that can be divided in three:
1) Utter fiction that is in no conflict with the rest of the utter fiction we get in Trek.
2) Utter fiction that was written with A in mind, but thankfully so ambiguously that B is also allowed for, as necessitated by the rest of the utter fiction of Trek.
3) Utter fiction that clashes badly with the rest of the utter fiction of Trek.
Anything having to do with nonfiction is quite irrelevant in that episode, really. Nobody was ever expected to think that Earth would really have a big war with supermen in the 1990s - everybody was simply expected to accept that it would happen in this piece of fiction. The same with all aspects of the spaceflight there: cryosleep and advances in interplanetary propulsion were not predictions by RAND or NASA or DARPA or whatever, but sheer fiction, a bit of worldbuilding that only much later bore fruit.
A 1990s introduction of DY-100 for interplanetary missions that took years and involved cryosleep to facilitate such durations fall squarely in category 1. Sure, we might argue that the propulsive performance involved would actually allow for shorter missions - but that is no reason to think most missions would not have been longer, for greater return.
A separation of 1996 and TOS being guesstimated as two centuries is category 2 stuff. But rather than move either of the endpoints, which have since become quite fixed, we can simply argue that two centuries was a slightly low estimate, a mistake or a deliberate probing lie by Kirk. Or that the 270 years that passed involved Khan sleeping for less than 250, possibly because of Einstein.
Little is left in category 3. ST:ID suggests that cryosleep would have disappeared with the introduction of warp at the latest, but VOY "11:59" contradicts that with a story of cryo-colonists from 2210. It's a bit odd that McCoy would be so out of his depth with the cryo-pods of CumberKhan, when his starship could well be expected to run into cryo-colonizers in the mid-23rd century still... (And never mind that the Botany Bay had shelves, not pods, for her sleepers.)
But there's fun to be had with all categories, speculation-wise. Yes, we know precious little about the circumstances of Khan's launch. No, he probably wasn't attempting to colonize a faraway planet - when Kirk presents him with the idea at the end of "Space Seed", he's just plain surprised. Yes, Spock's argument that nobody would waste a spaceship for banishment or execution is solid. So did Khan himself launch - perhaps with the idea of using his ship's automated CQ as a lure to hijack a more advanced ship in the upcoming centuries, for a glorious reconquista of Earth? Or did one of Khan's fellow Augments shoot the boss man out of Sol, in a move that was neither purely hostile nor purely benevolent (as evidenced by the choice of the name for the ship in which this mystery fellow stacked the sleepers)? Just about anything is possible, thanks to the "missing records" and the ambiguity of the writing and the innate dodginess of Khan's character.
Timo Saloniemi