I wonder if this is an aortic stenosis type thing? In the heart when the aorta gets too fat the blood flow changes from laminar to turbulent, and significantly reduces the flow. In your close-coupled empty cat the increased diameter is probably enough to cause the trip from laminar to turbulent, but when the matrix is in, the flow is laminarized. I would expect if this is indeed the case then fitting a thinner exhaust pipe as used in the CF2 will increase the exhaust flow by keeping the gas reynolds number the correct side of the transition. Reynolds depends on diameter, speed, viscosity, and density, so you could be going back and forth over the transition at different loads and engine speeds, which seems to be what you are describing.