the EGR valve acts like a median between intake and exhaust pressure. Obviously when exhaust pressure is high and the egr valve opens that pressure will flow towards the intake side. Ideally you always want EBP higher than boost. When a 6.0 overboosts you will often times get a popping through the exhaust which is boost pressure blowing back through the EGR valve.
The PCM constantly monitors EGR flow and will command VGT duty cycle to optimize exhaust backpressure which in turn helps promote EGR flow.
The MAP sensor is the primary input to the pcm for turbo boost. it can monitor boost and vary the VGT to keep it under control, it's when the VGT sticks that the PCM loses control of boost pressure and an overboost condition can occur