Kevin,
Well, rats.....you have a Flowscan and I have an EI, so no direct comparison.
FWIW, my red cube is much lower on the firewall. There's an elevation rise between the AFP pump and the point where the line penetrates the firewall with a 90 degree bulkhead fitting, then a level run through the red cube, then another elevation rise to the engine pump. I didn't want anything to trap an air bubble.
I called EI today and asked about an increased GPH indication with electric pump usage. The tech with whom I spoke said they want the red cube installed downstream of all pumps. With an FI installation they prefer it between the servo and the flow divider.
In the case of an installation like mine (FI, with the cube between the pumps)his explanation for increased GPH indication with boost pump operating was something along the lines of "pressure pulses cause the impeller to move backwards and count additional breaks in the light beam". However, he didn't have a clear explanation for the source of these pulses. I would point out that pressure pulses would do nothing. The fluid (fuel) is nearly incompressible, so reverse movement of the impeller would require actual reverse flow.
He had no clue as to why the carb guys would see a fluctuation with the cube mounted between pump and carb. It is their prescribed method.