Hey don't blame this mess on our base maps.
The JB4 PI mapping and BEF is doing exactly what it's supposed to do. Your PI signal from the controller to the JB4 verifying proper injection is solid and as a result high fuel pressure is holding steady. Fuel trims are within range. Everything points to the correct PI volume being injected. If you do need to adjust the PI volume for any reason or to experiment just raise or lower the by RPM adjustment levels on the user adjustment page.
The problem I see with this car is unexpected timing drops for the boost/power/fuel being used. And the mystery sputter you seem to have on spool. And as to the cause of those issues I'm not sure yet. You need to experiment to find the cause or as you've done hire a tuner to dig in to the car for more personalized assistance. As a first step I'd detune the car until you get consistent timing performance and then work from there.
Another idea is to disable the BEF hybrid spool mode, maybe one of the VANOS changes is causing problems with this manifold. Easy to test! As I suggested via email since you are basically developing/testing this setup get yourself familiar with TunerPro to make those simple changes. It's really easy stuff. You can change it faster than you can do a log to verify if it worked.