We really didn't get the opportunity to learn what the details of the implementation would be. And frankly, neither did Cap, he just dismissed it out of hand, and even when he seemed to be coming around, he dismissed it again because Tony had put Wanda under house arrest...which seemed like a massive overreaction.
But either way...again, if Nigeria doses't want the Avengers operating within their borders, that is their right. The Accords were a way of legitimizing the Avengers and allowing them to continue operating legally.
No, the Accords were a bunch of paperwork to regulate the Avengers. Have a governing body overseeing the actions of the Avengers, to take accountability and assessing threats an determining who and where each Avenger would be deployed. I get the appeal of this, but under that lies a ton of politics, agendas and lobbying.
You can rest assured the world would've reacted negatively to Crossbones walking in Nigeria, taking a vial of bad stuff, and going back underground. Headlines would scream "WHERE WERE THE AVENGERS?".
What I described is not some pessimistic view on bureaucracy, it's how the UN actually works. It's slow, cumbersome and a geopolicitical minefield. By the time they've reached a decision on whether or not to deploy the Avengers, the villain has destroyed or conquered the world two times over.