When the cylinders are shut off only two of the four primary exhaust pipes (#1 through 4 in the CS diagram) are used because there is no ignition in those cylinders. (cylinder 1 and cylinder 4 get shut off)
Because there is no ignition there is no exhaust pulse traveling through those two pipes. Those unused pipes create what is virtually an empty chamber, and exhaust pulses from the active cylinders will travel up them then echo back into the exhaust stream, causing a reversion-type obstruction to the flow from the active cylinders. If those two pipes are closed off at the collector where the flow from all four pipes enter the exhaust system, the flow from the two active cylinders will be normal. I assume that the shutter assembly the tech referred to would be placed somewhere between the primary collector and secondary collector where the flow from cylinder 1 and 4 enter the main exhaust stream. Since exhaust gas velocity is critical to the operation of the SkyActiv engine, anything that restricts the flow will reduce gas extraction from the cylinder, causing cylinder temperatures to go up and leaving residual unspent fuel in the chamber. This causes knock or pinging, which, when detected by the knock sensors, causes the ECU to pull engine timing until the knock is gone.