Close, it's pollution. An extremely lean state of tune DESPITE having a very restrictive aircleaner and mufflers insures that you're burning as little fuel as possible, thus creating as little pollution as possible. Even with this state of tune, HD's are riding the fence on pollution regs.
Yeah, most bikes (and cars) are running leaner than ideal for power to meet EPA regs. Even modern-design liquid cooled bikes like mine with fuel injection are still running way leaner at some rpms than is ideal.
But the restrictive pipes and air cleaner are more to meet the noise regs, aren't they? You can probably leave the bike stock except for rejetting and improve drivability a lot and improve peak power a little. But for serious power gains you need more flow - pipes, air cleaner, maybe cams (which were also chosen with pollution in mind, no doubt).