The devs get kudos for picking 12,000 years ago for when the Shard Split happened. It's recent enough that the geography of the the different Shards would be very, very similar to the Source (minus all the effects on the Source because of Calamities). It is is also long ago enough for every Shard's cultures to be completely different from the Sources. Take out Omega and Midgardsormr's influence on the Shards and they would turn out very, very differently from the Source even though they do have similar land masses.
There's also the fact that the zones we go to are the last parts of the Shard that are still around. The 1st Shards' equivalents of Ilsabard and Othard have probably been Flooded with Light and no longer exist. We're basically in the 1st Shard's version of Eorzea with totally different cultures.