Visibility on a map has no bearing on whether a territory would be recognized as independent from other recognized nation-states. For that you need political capital.
Vatican city, as the residence of the Pope, and pillar of catholic authority, has had ample supply of political capital through the formative centuries of European development. Though it probably has less power now, the sheer weight of institution, along with the personal value of hundreds of millions, if not over a billion people around the world, so give it a measure of authority. Any country so inclined faces steep international backlash should they wish to annex Vatican city unwillingly, and why would the Vatican give up their independence willingly?
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