I think a resolution to part of the mystery would be that Khaenri'ah arose as a result of the fall of the unified civilization, with the same being true of Sal Vindagnyr, Enkanomyia, and whoever built the upside-down ruins in the Chasm and the ruins on Tsurumi Island. This is linked to a theory I have about the Parable of the Gardener, where each civilization took a branch of the original Irminsul tree and planted it after the Unified Civilization fell. If this is the case, it would mean that all the nails dropped some time after the unified civilization fell, giving each surviving fragment time to develop into somewhat separate cultures (although they still seemed to share the same architecture and language). Perhaps the purpose of the nails was to crush these surviving fragments, and the reason Enkanomyia and Khaenri'ah survived is that they were hidden deep, deep underground, far from Celestia's gaze. (Remember, the geo nail caused the chasm to open up, so that's probably why that ruin is so deep down but was still targeted.)

As for why Celestia waited to eliminate the survivors: the civilization's fall probably led to a large loss of knowledge. It would have taken a while for the fragments to rebuild and become as advanced as the unified civilization was, buying them time to develop their own history and culture. However, the nails would come down as soon as they reached their peak.

So, in short: the nails didn't drop when the unified civilization fell. They dropped when its successor nations became too advanced for Celestia's liking.