We have written a custom Tranform inspector with a few useful buttons. However, when modifying a prefab instance, this inspector does not show the bold override text, and does not mark the override with the blue line on the left side, they can only be seen in Debug mode.
Well, what exactly are you expecting as answer? You clearly did not pay attention to prefab overrides and maybe even forgot about multiobject editing. How should we know what you did in your custom inspector? All we can see is that you did not implement it properly.
For those functionalities implementing some context menu buttons may make more sense. The transforminspector is a quite complex beast. For example in animation edit mode the captured field are usually marked red.