I really can't answer that I don't know enough about the engine particulars to say if the stock head/manifold will be a big restriction or not. I do know that high EGTs are a limiter for output and cause the companies to run the tunes rich and cooler, but making less than optimal power.
According to the ideal gas law (PV=nRT) becasue of the exhaust gas cooling you should be able to flow more exhaust out of a given diamater exhaust pipe. But really we'll have to wait and see what APR can do. I suspect that for small turbo's like a K04 this should make the upgrade easier and cheaper. Might be limiting for bigger turbos, but I suppose a lot depends on the flow rate of the new head?
If Im reading what you are saying correctly,
PV=nRT is a massive over simplification of what is going on.
manifold runner doesnt determine egt. EGT is determined by fuel, timing, and boost(in this case) and the point relative to TDC that combustion occurs.
You dont want exhaust gas to cool. the hotter gas is, the faster it flows....so you want a given volume of gas to be flowing as fast as you possibly can to impact the turbo charger with maximum energy.
The more energy you have pre turbine, and the lower the pressure you have post turbine, (ie size of down pipe) the more power you will make. Obviously a given quantity of gas only requires so much pressure differential for max hp, so putting a 4" dp wont make more power on these cars than a 3", but at 600hp, it would and a 3" pipe would become a restriction.
You are correct, though, that potential will be in how well the head flows, but that changes nothing from current. By eliminating the manifold, you are getting the came combustion chamber EGT, but a higher EGT at the turbine, which increases efficiency.
One of the things I dont think a lot of people get is why the APR stage 3 kits work so well and cost so much. Its just a bunch of pipes and a normal turbo right? The difference is in the manifold. by keeping the runners short, and making them out of inconel they are able to retain enormous amounts of heat compared to basic schedule 10 or schedule 40 stainless. That manifold in and of it self is close to 2 fucking grand to produce. It is accomplishing almost the same effect as eliminating the manifold, in as much as the goal is to ideally reach EGT=X at combustion chamber and EGT still = X at turbine. As the gas travels it cools, so the closer you can get the turbine to the output source of the combustion chamber, the more efficient it will be.
hope that helps.