There is a difference only in purchasing method: while using business account the orders will wait during delay time (you can set it on global settings) for aggregation and will be purchased when their total will be 49$.
It's better to use Business account together with Prime account so if the delay time will run out the order will be placed by the system one by one through a Prime account without aggregation.

While using Business Prime the orders will be placed like with standard Prime account, one by one, without aggregation. Business Prime is just providing to increase the orders amount on Amazon, but for the sf system it has the same logic like standard Prime.