I'd use a recirculation valve because releasing metered air will cause air/fuel ratio problems. On top of that, you'll need to be able to adjust the spring a bit to where the valve will be constantly open under vacuum.
I believe the biggest reason they use a recirculation valve is to simply increase efficiency under part throttle/vacuum. Spooling characteristics won't change at all due to it being spun directly by the engine, unless the valve stays open then you'll see some issues.
I though most Eaton setups had an internal bypass setup... basically to where all recirculation is done internally where no plumbing is needed. Is this one not the case?
On the throttle body, I believe for the positive displacement s/c's to run properly, the throttle body should be before the s/c (i.e. throttle body, supercharger, manifold/engine)