Throughout Trek, though, stardates are generally sequential in number, so it could have simply been a in-universe case that we saw the episodes out of order (it's no secret that TOS's broadcast order differs slightly from production order).

It's just a way that Chekov
could have been on the
Enterprise with Khan. But even if you dismiss stardate order, it could have been just that Chekov was already on the ship during "Space Seed" and their encounter was offscreen. I think that's the explanation that most folks went with.