It is somewhat ironic that the UN does not make provision for its own status and perhaps it is worth bringing this to their attention.

Whilst you are correct of course to suggest that when in international waters you would be under the jurisdiction of the vessel's flag (although this raises many legal questions relating to extraterritorial jurisdiction, particularly where no flag is flown), with regard to the issue of sovereignty, the United Nations Convention on the Law of the Sea states that "No State may validly purport to subject any part of the high seas to its sovereignty."

So I suppose it depends on what distinction(if any) you are drawing between sovereignty and jurisdiction.

Given that the Antarctic Treaty for example does not ascribe sovereignty to any particular state, it would appear that sovereignty is not a criteria for inclusion in ISO3166. By contrast, various states could assert jurisdiction over individuals located in Antarctica.

Therefore perhaps the UN should list international territory as a separate entry, in spite of the fact that once there you may be under the jurisdiction of a particular state?