Not really a bug... not a show stopper, but a real UX pain point - when I use overrides to hide labels, ref, value etc I do so mainly because of the screen clutter. What I would really like to see is that the bounding box on a selected component is based on only the visible elements of the component. Overlapping bounding boxes can make it a nightmare to select the right thing.
I am not sure if the current way it works where the original bounding box is based on all the elements is the intended experience (hence the bug and not a feature request) - perhaps it could be toggle setting to "constrain bounding boxes to visible elements"