I'm still a newbie with these cars, but I've done this before on my Evo 8 and Evo 9. Both with the APS Twin Vent BOV.
It supposedly causes inconsistency between shifts. The computer is expecting a surge of unused air (boost) to be dumped back into the intake, so with that it sends sufficient fuel to compensate. However, when the fuel shows and the air doesn't you can get rough idle, or even stall out as it has happened in my experience. In order to prevent that you just need to have the car tuned for a VTA rather than the factory Diverter Valve.
Again, this is based on my experience with my Lancer Evolutions which were both manual transmissios and NOT the SHO's. I will say that the APS Twin Vent was adjustable in how much was VTA and how much went back to the intake. A similar design for our cars could give a good balance and may not need tuning.
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