The theory is the added back pressure will incease exhaust velocity at low RPM's for better scavenging of the cyliders at lower RPM's. Since the headers are designed large for maximum HP from the stock engine, that is how they get over the compromise.
Me personally, I plan to leave it all stock. It makes more power then I need on the street, sounds great without being excessively loud (don't want to attract attention to my daily driver), and looks better then any aftermarket exhaust I have seen for it.
EFI shouldn't make a difference with the valve removed. The carburation problems come from the pressure pulses that are inherent in the design of the engine. At some RPM's they are flowing the right way for a better air charge (why it is possible to get over 100% VE), at other RPM's that will cause the intake air to pass through the carb 3 times (intake, reverb out, then intake again) causing a very rich mixture. That is what the EFI prevents. The valve in the exhaust will not effect the pressure waves.
Those pressure waves are why exhaust lengths are so important.