may or may not be an issue, if is you'd something that takes into account rpm and boost pressure, I imagine most decent aftermarket computers could offer something like this, or if you run it with rpm only you would need a decent boost controller that can compensate for it, depends what is slower the wastegate actuator or the flap actuator, the fastest one should be doing the most control, I imagine the wastegate would be the fastest so unlikely it'd prove a huge issue.
Just means you'd need a competent tuner who can test all possible scenarios and ensure stable boost and no detonation, couldn't be too difficult.
I can't see backpressure being a huge issue, you'd just tune the gate to open slowly once full boost is it, cause if you did it too fast boost would drop/dip.