Thank you for reporting a bug to Unity.
After reviewing the behavior, it looks like the visibility and picking toggles do not prevent editing and making changes in the scene view, as other game objects are also still interactive after disabling both. so this is not the intended use for these toggles. i would suggest to avoid painting on overlapping terrain, or temporarily disable the adjacent terrain game object.
We will close this case as 'As Designed.' If you have feedback on how the feature could better meet your needs, please let us know - we value your input and consider it in future improvements.