This issue probably cause because of the instaced stereo rendering and the Sky Atmosphere system Just not implemented this feature yet.
I’m looking for ways to use Sky Atmosphere in VR. But couldn’t find a solution yet.
I believe Epic doesn’t want to spend resources on this topic since implementing such feature also requires a lot of creative optimizations for VR.
I hope they at least have a few personel on this topic or someone from the community looking into it as hobby project 