I wonder if having a cutout affects the flow when it's closed (versus no cutout). There's a y that some exhaust gas is going to fill. I realize that once the y is filled with exhaust, it can't fill any more, but I wonder if it causes some turbulence there that messes with the rest of the flow.

 

Im sure it does cause some turbulance but most of the exhaust gas is probably going to take the straighter path out through the cat-back it you have it on the i-pipe, but if you place it on the y-pipe where it bends im sure that would cause some more turbulance. I dont think its anything to be worried about though.