i wouldn't go so far as to say its a "myth." yes, a more freeflowing header and exhaust is great, but why doesn't every aftermarket exhaust come in 3 inch trim diameter. its because too much flow can change the combustion cycle by creating too much flow. this will lead to reduced power in lower rpm's.
as is the case with most applications, a compromise is best. stock exhausts are designed for the consumer wanting a quiet, yet efficient design that serves its purpose well.