The below is as I understand it, so the theory may be wrong.. but here goes!
The logic applies when you are running a twin-scroll turbo and manifold.
The engine obviously has a specific firing order. In an open/single scroll manifold, some exhaust valves will be closing, when others are open/opening and expunging their gas into the manifold. These exhaust 'pulses' will, in a single scroll setup, interfere with one another and stop the flow of the manifold from being as smooth.
Firing Order: 1 - 5 - 3 - 6 - 2 - 4.
With a twin scroll arrangement, you separate the 123rd and 456th cylinder exhaust ports into two groups, thus the firing order of the engine means that the pulses of the exhaust gas do not interfere with one another. This pattern of separation also means that the timing of the pulses are equally staggered in each port bank, for one full cylinder firing cycle.
The idea of the twin waste gate setup, is to keep these two groups of cylinders separate until they reach the turbo housing/flange. With a single waste gate setup, you have to have both halves of the twin scroll manifold joined where they meet the waste gate...which will remove some of the positive effects of the twin scroll manifold.
In threory it makes a difference. The downside is: increased heat. More complication and less space to work. More to go wrong.
Personally I'm an advocate of the Twin scroll manifold, turbo, with one large HKS 60mm waste gate setup. Tried and tested by HKS themselves to ensure no boost creep, and in a test on supraforums by PHR(I think) the single waste gate HKS manifold out-performed the twin waste gate, all singing all dancing Full Race Model.