Either Both would make the same, or the one with the EGR would be on top. Not to mention the engine with the functioning EGR would get way better gas mileage.
The main difference with tuning would be the one with the EGR could run more timing, which usually results in better performance.
EDIT - Just noticed msilver response.
In my own words --
The air is replaced with exhaust that will not burn again. Because of this, and when introduced back into the combustion chamber, (replaces a small amount of incoming air) the combustion chamber temp is lowered. Because of this new lower temp, more timing can be run. And because more timing can be run, more performance and better gas mileage is achieved. This new lower temp, more timing combination USUALLY offsets the more air, more gas combination.
So my vote is for the engine running an EGR valve.