Africa has been a continent in turmoil for a long time. Because of this, the majority of countries in Africa are unstable, without an effective governmental system. It would be easier to keep track of people who were moving about the continent if everyone had a passport. Because of the lack of organization in some countries, it might be easier to just have one passport for the whole continent.
To a certain point, I think that Africa is still a developing nation. I'm glad that Africa is taking a step towards diplomacy, and that they are stepping towards more rules, regulations, and opportunities. "single African Passports" can allow people to enter and exit Africa as they wish, allowing new business opportunities and more.
While unity seems like it would be a good idea throughout the world, at this point in Africa's tumultuous state of affairs, issuing a passport that allows all people to go anywhere in Africa will only exacerbate the problems. The best bet right now is for the government to lock down the bad guys and leave them locked down until they can sort it out. Do not spread the violence.
I actually don't think that the establishment of an African Union and single passport is a step in the right direction for the continent of Africa. All you have to do is look at the Brexit fiasco right now to see how these types of unions simply do not work. Countries deserve and need autonomy.