The deep 'drone' from the exhaust sounds to me like the gearbox retarding the ignition, as it should do, and sounds like normal operation to me. The exhaust note normally drops, 'farts' a bit, and then goes back to normal after the gear change.
Theres always going to be some release of boost pressure between shifts.. generally its not noticeable, but with an aftermarket BOV it may be exaggerating it a bit. Dont forget that the gearbox retards the ignition.. you cant expect the turbo to still be producing max boost during this. Your description sounds like normal operation.
On an auto i'd personally stick to the stock BOV, as autos do funny things to boost pressure when changing.. probably most aftermarket BOV's are made for on/off boost pressure that you get with a manual.
PS im probably technically incorrect, but it kinda makes sense.. i think, maybe...