But that's a line of dialogue from another timeline, in a story that never happened anymore.
And the divergence point between the timelines was 2233, as I'm sure you know. Khan is from well before that point and so he should have started out as the Khan we see in
Space Seed.
And, honestly, the whole bit about Khan being a Sikh comes from just a couple of lines of dialogue in "Space Seed"
Does it have to be mentioned in every scene to be considered canon?
No, but Khan's nationality was hardly the point of the previous versions nor the essence of the character. And, just to put things in perspective, do we really think that casting decisions ought be based on a couple of lines of dialogue from a fifty-year-old TV episode that most of the movie-going audience probably hasn't even seen?
I'm inclined to just chalk it up to poetic license.
A weird analogy: In
The Bride of Frankenstein (1935), Dr. Frankenstein's fiancee Elizabeth was played by Valerie Hobson, replacing Mae Clarke who had played the part in the earlier 1931
Frankenstein. The two actresses looked nothing alike. Clarke was a platinum blonde, while Hobson was a striking brunette.
Should
Bride have included a scene explaining how Elizabeth had somehow gotten plastic surgery and a makeover? Even though
Bride picks up only minutes after the first movie ended?
Or did the filmmakers just trust audiences to understand that, at the end of the day, these were theatrical productions and, hey, we're all going to pretend that we didn't switch actresses and that Elizabeth has
always looked like Valerie Hobson.
These are movies, not historical documents. It's all smoke and mirrors . . . and "canon" is an illusion.