OP here, cool to see this thread getting traction. I actually do have an update as of very recently.
This problem had persisted for me through V2.4 of the APR tune, and the oscillations started to get pretty bad and overall off-boost performance was pretty crummy. I was getting boost oscillations even going from coast to WOT above 4k RPM, and it seemed to be taking longer than it should to reach peak boost, and would hunt and oscillate on its way there.
Then recently Arin posted in the massive APR Stage 1 V2.0 thread about an example where someone having issues like this was able to fix the issues by thoroughly checking for boost leaks, particularly PCV-related issues.
I said to myself forget this, let me go in and make sure that everything in the engine bay that I've touched has been really torqued down well enough. I'd replaced the PCV plate and had previously cleaned the IAT sensor, so I added about a quarter turn more to every bolt on the PCV plate (stopping short of uncomfortable tightness) and the bolt on the IAT sensor. I also re-checked the spark plug torque, since in the past I had issues with not quite enough torque there, especially after being dumb and re-using the crush washers after checking the plug gaps.
Although I'm really hesitant to believe it, it honestly made a pretty massive difference. Boost oscillations are pretty much gone, and off-boost behavior is way better. I strongly think it was something about how the PCV plate was mounted that the car wasn't happy with, and it was probably affecting how the PCV system operated and possibly allowing boost to go where it shouldn't, or otherwise messing things up.
Check the simple stuff first. I swore up and down that it was the tune and was ready to drop $650 on a Cobb Accessport with a Stratified tune.
Do I think APR's wastegate PID tuning needs refinement? Sure. Could things be made even a bit better by replacing the N75 anyways? Probably. Sometimes boost onset feels a little too muted, and sometimes engine braking isn't strong enough, and sometimes the throttle pedal response isn't perfect at low speeds (tune imperfections). But simply re-torquing everything down seems to have largely addressed my issues. I hate that that's my answer, but that's what it is.
Time will tell if 1.) this was a real fix and 2.) if symptoms will return. But let me tell you this: I was reluctant to have friends drive the car because it felt broken and like there was only a vague suggestion of a relationship between the accelerator pedal and what the car was doing.
I now wouldn't hesitate to hand the keys to my car enthusiast friends and have them hoon it. They'd probably note how the suspension and bushings are getting sloppy after 143k miles, but that's a different problem space.
Do the easy stuff first, and double-check everything you've touched. Err on the high side of torque recommendations.