Absolutely, that's a major thing.
I say that because it's important to know that if you meet two people from the south, one of them is more likely to be Ugandan. But you could say I'm a Nuer, I'm a Dinka, I'm a Shilluk, and so on. That's a big problem, actually, because there is no way to identify the southerners exactly, especially on the borders of these countries: Sudan, Uganda, Kenya, and the Congo. These borders are not monitored. There is no exact border monitoring, and people enter here and there and move here and there. The movement in one way or another is also a problem.
So I agree with you that these people will be in a dilemma, unless the government of the south says, okay, you are southerners, come in just for political matters.