There's no perhaps about it, your trim disparities had nothing to do with the differences in airflow between the front and rear inlets. Coincidence /=/ causation.
I don't know a whole lot on N54 specific tuning, but you mentioned it happened when you raised boost. As overall pressure, and therefore airflow, increases, the disparities between individual cylinder airflow are magnified accordingly, and thus fuel trims would get further and further off as you increase boost/cfm.
Keep in mind I am not totally disagreeing with you....
Your leaving out another factor. Not only did it happen when raising boost on the "previous setup", it does not happen on the "new setup" pushing more power = more strain on the fueling system ever if I increased boost, richer fuel, the issue does not repeat as it did on the previous setup.
So what I am looking for is a "constructive" reason why then and why not now. The easy way out is when it makes no logical sense to say it was something else but not have a spec of theory of what that something else could be. When we conclude to this then we really dont understand things between hardware and DME logic.