Those are very valid points, Portmanteau - but at the same time they do not account for all of the subject matter in discussion in this corner of the thread. Yes obviously there is a highest-ranking authority in a given sovereign nation .... but it does not necessarily follow that military commanders will be subservient to and compliant with lawfully constituted sovereign authority. For brevity, I'll simply cite "military coup d'état". And, in some countries even without power concentrated in its military, the civil authority may be a figurehead more than a real decision-maker.
More generally, is it not the case that where a "standard" air defence rule of engagement would activate a scramble to ident, this action does not require the okay of the leader of the national government? In other words, the existence of a head of a country's national government does not either mitigate, or erase, the relevance of the larger question - how should the worldwide civil aeronautics regulatory system improve its interaction with air defence authorities (where such defences exist)? - or the more particular one - should signatories to such worldwide system be strongly encouraged not to give both the defence and civil aviation portfolios to the same minister?