Ah, I forgot that the S5's have a boost control solenoid from the factory. If you're using an S4 ECU, then you won't have the control output needed for this and should just cap the extra nipple (yellow circle). For an S5 ECU, this should be hooked up to a solenoid valve that is controlled by the ECU to dump some of the boost "signal" to the wastegate, allowing the turbo to build more boost at lower engine speeds (basically PWM to reduce the pressure trying to open the wastegate).
With the routing you were talking about before, it would definitely cause idle issues since air could essentially bypass the throttle plates by going through the solenoid valve, causing a leak of metered air (so no lean condition, just a high, possibly hunting idle)
Is the boost control solenoid the switching solenoid that you're talking about (in your third paragraph)?
You can ignore the twin-scroll actuator - either wire it open or cut off the arm and plug the hole in the manifold completely.