Sorry, it's been many years since I last saw TWOK. But my point stands in that it was "Botany Bay" that jogged Chekov's memory, not the planet's designation.
I agree with this completely. Also, I don't know how the planets/systems are numbered, but Ceti Alpha sounds very generic to me, add to that the "one dynoscanner" barely showed any lifeforms, it probably never crossed his mind.
Finally, Kirk giving Khan exile was (probably) really against regulations and I don't think it would have been very publicised, Chekov, if he was there, may have experienced the whole thing but didn't know what planet they were left on, not being the navigator at the time.
Also, this is a stretch, but Khan had free access of the Enterprise Library, might that have included Starfleet personnel records? Could he have seen Checkov without him being there in person? Maybe Khan has a photographic memory, he certainly learned how to overload the engines.
I just don't see it as that big of a deal about Khan knowing Checkov because in the first episode produced with him, Catspaw, Checkov said "I'm no that green." As he was new but not that new, he may have been around a few months and we just never saw him on camera. They don't pull 24 hour shifts on the bridge, do they? There needs to be relief crew when the episodes aren't happening.