airraptor, I've never tried a GYT-R head pipe I'm just telling you how mine works.
It still makes sense to me that the larger dia head pipe would flow better.

I'm new to 4 stroke quads but have been building hi performance VW's fo over 20 years & even on a stock motor a larger header pipe makes more power than a stock dia header.

 

I think what airraptor is trying to say is too large of a header slows down exhaust velocity which prevents complete cylinder fill for the next cycle which robs power. It's important to have high flow, but it's just as important to have high exhaust gas velocity. The most sucessful head pipe design for Yamaha's four stroke dirt bikes incorperates a "stepped" design starting with a smaller diameter tube closest to the exhaust ports and stepping to progressively larger tubes as you get closer to the silencer.

 

I've always ported my VW heads Intake manifolds & intake ports for velocity not just hogging them out to make them as big as possible, but the intakes are ported more towards volume (not overly so but more than the intakes).
I may be wrong & correct me if I am but don't you want the most flow possible without losing backpressure in the exaust since the piston forces out the exaust gasses, & isn't cylinder filling more a function of valve overlap than scavanging?