The resonating back wave from the convergence cone is what is really supercharging your engine. Header length plays part of the role of how that wave is timed with the engine. Basically, it changes the RPM range of the pipe.
If you take a look at some examples of tuned pipe theory you can see that the formulas for designing pipes have variables for header diameter and length, divergent cone angle and length, belley diameter and length, convergence cone angle and length, and stinger diameter and length. Basically, what I'm saying is that you can change the header length and yes it will change the tuning of the pipe, however, if the pipe isn't designed for it, you can actually lose alot of performance. Examples of pipes that shouldn't be touched are the short compact pipes for the HPI Baja such as the Jetpro track pipe and GBE Hornet pipe. They've setup the divergent and convergence cone in a way to work with such a short header. Extending a header on a pipe like those to a somewhat standard 8-9" range like you see on full size pipes would actually throw those pipes so far out of tune that you might as well run a stock can.