Just finished adding an Aircharge Multiplier to all of the 2011+ definitions. On every car I have looked at, this multiplier is set to 1, with the exception of the Boss 302 calibrations, and the Roush supercharged Mustang files. That is why I decided to add this parameter.
In the past, tuning a blown 2011+ Mustang has always been easiest starting from a Roush calibration. I always assumed there was some parameter I couldn't see before, and I think this it. Both the Load at WOT (not in other tuning software) and Aircharge Multiplier are raised up, and this can probably explain some of the weird issues you may run across starting from a factory calibration when adding boost.
First image is an N/A vehicle
Second image is a boosted vehicle