On my computer with Unity 2019.2.9f1 and Vuforia 8.5.9
If I switch from Android to iOS, the Render Over Native UI is automatically set thank to this script
Vuforia Engine: Automatically enabled "Render Over Native UI" in Player Settings when switching to iOS because of known performance issues on ARKit-enabled devices without this setting.
UnityEditor.Build.BuildPipelineInterfaces:OnActiveBuildTargetChanged(BuildTarget, BuildTarget) (at C:/buildslave/unity/build/Editor/Mono/BuildPipeline/BuildPipelineInterfaces.cs:412)
However, it doesn't seem to be triggered using Unity Cloud Build when targeting iOS.
Temporary workaround: create a branch in the sourcecontrol (git) and applied the change manually (ProjectSettings.asset, preserveFramebufferAlpha:1) then start a Cloud Build for this branch when an iOS build is needed.