In both normal Studio editing, and Play-testing, the ‘Atmosphere’ effect doesn’t reflect the rotation of the skybox if it’s been rotated using its SkyboxOrientation field.
(in Edit mode)
I’m experiencing this issue as well. I will probably work around this for now by importing the skybox into Blender and reexporting with the desired orientation, but this is definitely not expected behavior.
EDIT: I see that this is the documented behavior of reflection probes. However, I am never changing the orientation of the skybox at runtime, so it is still unexpected that the reflection probes would use the unrotated skybox despite it never being unrotated.
If this behavior is to stay, perhaps something like Lighting:ForceUpdateReflectionsSlow() would make a good API addition for edge cases like this? The reflections are dynamically updated when you swap out a skybox anyway, so allowing more granular control would be excellent.