I take it from the post that you finished the last puzzle?

I'll point out that the VV3 villagers came from the VV2 settlement, and the VV2 settlement was founded by villagers from VV1's settlement, and all three exist at the same time on this island.

The previous inhabitants who built the secret city have obviously been buried long enough for their works of stone and rock to fall into ruins and disrepair. I don't think any of these villages were part of the magic or nature tribes described by the story.