Do you think that in the new world (if you were to beat the game) Skaia would still have influence, or that the Godtier could commune with it after the game?

Skaia doesn’t influence, it only Sees and Knows. As we have already talked about today, like a big blue perv. Furthermore, the Clouds are gone after the Ultimate Alchemy, so no future visions for you. “Communing” with Skaia really sounds like simply having a Light Player- Likely a Seer or Mage of Light, and still I’m not sure that counts as ‘communing’.