No, it is the TC and not unlocking on the 3-4 shift that is causing it and that is all in programming. About all you can do is get a feel for when it wants to shift to OD and lift off the throttle a bit so you don't have a lot of exhaust flow that drops suddenly, or, manually shift to OD when you are up to speed and off throttle.
What is happening is the exhaust flow is dropping because of the big RPM drop and fueling cut from 3 to 4, the flow won't support the turbo speed so it literally stalls the turbo compressor because boost is suddenly greater than drive pressure. If you could tune the 3-4 shift to unlock completely, shift 3-4 and keep rpms up, then lockup the TC when things balance out it won't happen. The 3-4 lockup strategy pulses the unlock and expects a single disk that will unlock enough to do that, but, a triple disk will not unlock on a TCC pulse off. Not enough time to get it to happen unless the pulse width is lengthened. There is a possibility that custom trans tuning can address that, have not aske the authors whether that specific PID is exposed and they can adjust it. The 48RE transmission controls are kind of crude and they are not exposed or documented well.