... because not all souls get plunged into the depths of the Aetherial Sea and blended up. Strong-willed individuals don't go too deep and are reborn.
The Ancients we meet who comment on our soul "color" also don't say our soul is exactly the same, just very similar. Perhaps that's due to dilution, but perhaps that's because even Azem wasn't able to fully avoid the pull of the Lifestream.
Regardless, that doesn't preclude the planet creating new souls, something from the Ancients' plan to sacrifice new ones to Zodiark for their brethren's back in return hinges on.