Matching numbers in the ECU is not the same as actual boost. What happens when you input 100% in you WGDC at WOT? What exact routing did you do? What was your spring pressure?
The whole idea of the hybrid setup is using the MBC at WOT for boost control, yet maintain a car that does not PTFB during cruising. If you're not doing 100%, why put a MBC in anyway? Once the throttle goes to the floor, the EBCS is completely taken out of the loop as it flips to the port that is capped off, thus forcing everything through the MBC as if the EBCS was not there. The EBCS should only have control at PT conditions where you would build boost over what the WG spring pressure is. If you run a low enough spring setup, you could virtually have LOTS of boost control at PT, however, with the MBC in parallel and no other exit (not VTA or inlet on the 3rd port), it will ultimately cap max boost if for some reason high gear/high load would give you PTFB from a tune that would otherwise not be hitting boost targets.