The overrides are applied correctly, but immediately after saving the Prefab it is changed in memory which results in showing the overrides as not being applied. This happens in Assets\ThirdParty\Photon\PhotonUnityNetworking\Code\Editor\PhotonViewHandler.cs:OnHierarchyChanged()
It seems the implementers this library explicitly edit the Prefabs in memory without saving them which makes any apply operation for PhotonView.ViewID and PhotonView.sceneViewId look as if it's not working.