Because the dialogue has to be taken with a grain of salt based on Spock's "fragmentary" records line, the fact that to control a quarter of the planet one would have to be ruthless to some degree and how we see him treat the crew of the Enterprise.
Oh, cripes. Here comes my infamous quoting machine again.
SPOCK: However, scanners make out a name. SS Botany Bay.
KIRK: Then you can check the registry.
SPOCK: No such vessel listed. Records of that period are fragmentary, however. The mid=1990s was the era of your last so-called World War.
*Later*
SPOCK: A strange, violent period in your history. I find no record what so ever of an SS Botany Bay.
Sounds more like ship records than actual historical records given how whenever a character talks about Earth history, they seem to know exactly what transpired.
MCCOY: The Eugenics Wars.
SPOCK: Of course. Your attempt to improve the race through selective breeding.
MCCOY: Oh, now wait a minute. Not our attempt, Mister Spock. A group of ambitious scientists. I'm sure you know the type. Devoted to logic, completely unemotional-
KIRK: An improved breed of human. That's what the Eugenics War was all about.
SPOCK: Your Earth was on the verge of a dark ages. Whole populations were being bombed out of existence.
SPOCK: In 1992, a group of these young supermen did seize power simultaneously in over forty nations.
KIRK: Well, they were hardly supermen. They were aggressive, arrogant. They began to battle among themselves.
This one is my favorite because it pinpoints exactly where the fragmentation occurred and why.
SPOCK: I have collected some names and made some counts. By my estimate, there were some eighty or ninety of these young supermen unaccounted for when they were finally defeated.
KIRK: That fact isn't in the history texts.
There's a mystery here for certain, but it doesn't involve Khan's rule of Earth. That is clearly well documented judging by how familiar the characters are with Khan already. So what answers does Kirk seek?
KIRK: What was the exact date of your lift off? We know it was sometime in the early 1990s, but
KHAN: I find myself growing fatigued, Doctor. May we continue this questioning at some other time?
KIRK: The facts I need, Mister Khan, will take very little time. For example, the nature of your expedition.
KIRK: You fled. Why? Were you afraid?
KHAN: I've never been afraid.
KIRK: But you left at the very time mankind needed courage.
KIRK: I'd like those answers now. First, the purpose of your star flight.
And what is the first question Marla McGivers asks Khan?
MARLA: I'd like some historical information about your ship, its purpose and
There you have it. The only bit of history involving Khan that isn't reliable involves how he and his followers fled Earth in a sleeper ship. That's the only mystery that the crew can't explain, and it's the only thing Kirk wanted to have answered. So no, I won't apply the "fragmented records" line to exonerate STID's stupid attempt at solidifying Khan as just a bad guy who wants to kill people because that was not the point of Space Seed's story.