I played briefly with a VR setup at work, where we were visualizing internal airflow inside a car. Does the air make it from the front to the back? It was a totally natural feeling to turn and look where the air was going; I was holding a 3-D "air mouse" in each hand, each with a trigger/button.
My initial thought for a Civ game would be to "walk" through and over the map. See your cities, yes, but also see where your units are deployed. Many times -- in both Civ6 and earlier games in the franchise -- I have clicked on the wrong unit when engaged in battle. Being able to move my view point, to see the city that I'm attacking, to clearly see the AI units defending and their health... well, that would be cool. Hearing a countdown, turning to watch one of the space missions launch, that would be cool. Pick up a governor from one city, dropping the governor in the new city. Both handheld devices, and their buttons, could be used for interacting with menus. The whole UI would need to re-thought and adapted.
I also realize that these scenarios don't happen every turn. Especially if the player is pursuing a diplomatic or religious victory, the ability to "stride like a colossus" over the map may be less useful. On balance, it may not make sense to develop a 4X game using VR tech for everyday play... "just one more turn"... the way that Civfanatics like to play.