To help support exactly what Jerry said, there are two-stroke porting and expansion chamber design software programs out there. They don't take into account every little factor, but they do a good aproximation.
With two-stroke pipe software, you can create artificially high HP numbers using small stinger diameters. In actual practice this results in overheating, so there is a discrepency between calculations and real-life applications, but the THEORY is still sound, stinger restriction is a very important aspect of pipe design.
Restriction has a variety of factors, the largest being diameter, but length and path are also important aspects, and that's the biggest difference between the in-frame and out-of-frame pipes. The in-frame pipes have both a shorter length and less restrictive path, making them better for the bigger bores that need that extra flow, and actually worse in many situations for the stock and small-bore engines.