Permanently? Or will they get FC later?
There are two differences, you can sign up for a main country i.e 1 of the test nations (Aus, Eng, Pak, Sri, Ind, Saf, NZ, WI) and they all have FC, OD and T20 tournaments. Where as if you sign up to a lesser nation (Kenya, Afghanistan, USA etc) then all you will get is OD and T20 games.
The advantage of a lesser nation is you get into it quicker as their is smaller waiting list, but the disadvantage is that you won't get the FC or the same amount of income.