The Stock pipes direct cylinders 1-2 to one side, and cylinders 3-4 to the other side. Due to the firing order, the exhaust pulses end up with a push-push-wait-wait in each pipe. Combining 4 to 1 changes this to a push-push-push-push (i.e. a constant flow of gas, as opposed to a double push/double wait). I would guess that this helps improve the exhaust flow characteristics, although at 4000 RPM you are talking a minimal difference (which may be statistically significant, however). Based on reports of those who have went 4-2-1 with the Connie, this does seem to help performance.
What I've been wanting to do is change the pipe routing to 1-4 left 2-3 right, so that the exhaust pulses are evenly spaced, yet you'd still have a dual system. I'd be curious as to how this would compare versus the stock setup or 4-2-1 setups. However, this isn't currently in the budget; maybe if I hit the lottery...