Here’s my theory on the Khan situation:
1. Khan came from a PRE_warp civilization , technically speaking. Yes, it was EARTH , but in the past.
2. Therefore the Prime Directive applies. Khan and crew were on a planet with all they needed to survive (based on current circumstances). However, no warp speed tech available to them. So the Federation was “safe” from them, and could perhaps much later send an observation team. But no further interaction needed for a while
3. Starfleet & The Federation are cool with that. Charts are recorded accordingly, along with general info on the other planets. Enterprise did NOT explore the other planets, other than no apparent intelligent life
4. Either some kind of weird disaster, or some illicit mining or science experiment creates a huge explosion on Ceti Alpha 6, sending it out of its regular orbit, such that 5 & 6 switch places, essentially
5. Khan feels the shockwaves and sees lots of meteors, perhaps a few huge ones, that decimate the planet and create the deserts. From HIS perspective, it seems like Ceti Alpha 6 exploded (perhaps the meteors came at night, so that he was able to calculate where it came from… maybe even saw the explosion in a telescope, or the meteors coming from that direction
6. Khan comes to the conclusion that Ceti Alpha 6 completely exploded. However, for Starfleet, they didn’t know the difference
7. Kirk becomes head of Starfleet Operations and authorizes the Genesis project. He is kept up to date with the progress, and approves Ceti Alpha system as a possibility to explore. However, the Ceti Alpha 5 quarantine due to the Prime Directive is listed. Therefore, Ceti Alpha 5 is not considered. Ceti alpha 1-4 and 6 are options
8. Reliant goes to what they think Ceti Alpha 6, since it is listed as a possibility. They COMPLETELY ignore what they think is Ceti Alpha V, because it supposedly has life on it, and therefore completely useless to their mission Checkov and Terrell beam down because of a faint life sign, unaware WHY there is life. And there we go….