You can't pin down a preposition like this in idiomatic expressions. When eyes (the most common perpetrator) 'glaze over' nothing covers them (as when 'her hair flopped down over her eyes'; it just becomes obvious that the owner of the eyes is thinking about something else.
'Bubbling over' can refer to a liquid coming to the boil and spilling over the top of the pan, but it can also be used metaphorically about high spirits or excitement. In both of these cases I suppose you could argue that the 'over' means 'beyond the scope of the container under normal conditions' ['normal conditions being, in the case of the pan, no heat; and in the case of the person, no emotional disturbance] - which is unlike the 'over' in glazed over - but I think that sort of argument is dry and lacks insight. What means something is the phrase, and the phrase only means what it means when it is given a context (in the broadest meaning of context - not just surrounding words but surrounding things and situations).