Steps to reproduce:
1) Download attached project " Unity5_BugReport_HideFlags_NotEditable.zip" and open in Unity.
2) In Project tab, click on 'Banana' prefab and check Inspector. You will notice that you can't edit this MonoBehavior(see attached image"one.png").
3) Drag&drop 'Banana' prefab in to Hierarchy tab and check Inspector. You can edit this MonoBehavior(see attached image"two.png").

Expected results: Inspector should obey the flags when prefab is in Hierarchy tab.
Actual results: Inspector isn't obeying the flags when prefab is in Hierarchy tab.

Reproduced with: 5.2.4f1, 5.3.5p6, 5.4.0b24