I'm curious as to whether the exhaust flap serves more than one purpose...

I realize it dampens the sound at under 3500 RPM, but does it also serve to keep TQ levels up at lower RPM? I have had several liter bikes that had the flap and for the most part, opening them at lower RPM's meant losing TQ at those speeds as well, due to the loss of back pressure. Any thoughts on this?

Nah, dyno tests show it doesn't make any difference or not enough, like on a bike. It's too far back and well after the cats, so it just doesn't matter. The flap is there for sheer flow volume only, not any extraction resonance issues.