You would need someone like
@jyamona to tell you for certain. He will know the source of the torque limiter signals.
From my first impression I'd say that's normal and related to the request for timing drop during shift. On the N54 there's 2 different torque limiter channels, one for timing and another for fuel and air, the timing one is normal during WOT upshift but the air and fuel one should only be active on shifts where the engine needs extra help to meet the requested RPM/Torque target, basically a throttle blip to ensure smooth shifts. On your N55 it may be that the TQ lim 3 param is the timing intervention and the TQ lim 2 is air/fuel intervention.
Your boost is 4PSI above target at some points, I'd be more concerned about that. Your throttle is closing to try prevent the overboost but not having much luck. Looks like the tune needs work.