> That said, the whole "let's run another referendum until we get what we want" approach doesn't endear the EU Council of Ministers or the Commission to me.
If someone offers you a cup of tea, and you decline, do you get offended if they then offer you cup of coffee instead?
Even if the question being asked were exactly the same, it would only be like a piece of software asking "Are you sure?" before you delete something, or providing a cancel button after the process has started.
I concede, though, that you're absolutely right about the supremacy of EU law being a principle clearly recognised by the ECJ. The difference is, by not putting this principle as an article to the treaty, it remains slightly less binding on signatories (under international law), since it relies on the evolving precedent of the court, rather than being agreed up front.
Now let me explain the logic of this supremacy principle.
If a sovereign nation agrees to be part of an organisation which creates laws that apply to its members, then those new laws apply just as a new law passed by a national government would apply. This follows the basic legal principle of "lex posterior derogat priori", but moreover there is the principle of statutory interpretation which means that a national parliament can't "accidentally" pass a law which contradicts existing EU law.
A member state, remaining sovereign, may choose to deliberately pass a law, knowing it will put them in breach of EU law, but that would also put them in breach of international law, which courts generally assume governments aim to avoid. In any case, it would be churlish for a member state to deliberately break the commitments it made as part of joining the union when there exists a mechanism by which it can leave and disapply all EU law.