Nice and ballsy with zeroing PID. Can you attached the ATR map?
Couple things I noticed... I expected WGDC base and "after PID" to match, but this is not the case. "Boost" channel is factoring throttle position (pressure differential)
If you had MAP and req MAP matching more closely before compared to the attached logs due to temperature I assume, then this would be a good time to play with the "Cyl Temp Comp" tables which I am guessing directly control WGDC per temps (FYI: I have not played with these). This way you could theoretically map WG per all conditions and PID would play a more secondary role in boost control.
Next logs maybe add WGDC temp