Those international bodies and agreements only have legitimacy because nations agree that they do.

To take a slightly different take, Mexico exists as an objective fact. The EU can decide not to recognize Mexico as a country but Mexico continues to exist and faces basically no adverse reaction from this. If the countries that make up the EU decided it was done and stopped acknowledging it, it would cease to exist. It has no population, no military, no land. No means of projecting force. Mexico retains these properties and abilities regardless of any agreements to the contrary, or lack thereof.

I'm not saying international agreements don't exist but that they have no inherent sovereignty because they are by definition but hand-shake agreements between independent sovereign members.