I recommend that you guys log TD integral and TD proportional using enginuity's latest defs. It will shed some light on controlling boost.
You should never allow it to overboost significantly. On a stage 1 or stage 2 car, the overboost is usually around 0.5 psi. So, the shape of the TD integral negative beyond -0.5 psi theoretically should not be that significant. I mirror the TD integral positive.
Use WGDC initial plus the TD integral to control boost. Don't overboost.
Here's a 2005 LGT Stage 1 (bone stock hardware) that I tuned for a friend. Sealevel in Hawaii. The blip in WGDC at 2400 rpm is my fault. It didn't affect performance but I cleaned it up later. The different curves are for different gears. Spool is affected by the loading (gearing).