The stock airbox and filter maybe slows the spool down enough to not over boost? Lol I have no idea but I'm pretty confused on this whole issue.
Have you taken my advice and logged as you do this?
You have to take note of what you are reading so u have a point of reference.
When you have the intake setup in that you are saying is causing issues
-map sensor reading
-wastegate percentage
-throttle
-afr
-timing
When you change it to the setup that you are saying makes it better. Compare the readings
You will find that doing this will narrow your results and help your diagnosis
Changing parts back and forth is fine and dandy, but what if you are just masking the issue
Overboosting can be cause by various things
Excessive exhaust flow (but your are stock so that's unlikely since your fuel maps etc. are stock)
Internal failure
Faulty map sensor
Faulty wastegate actuator
Faulty wastegate solenoid
The list can be carried on and on.
You need to be careful here because overboosting can really do some damage in the long run.
Post what you find and I will keep helping the best I can