I noticed on the Tanks,Inc. setups similar to yours, that they have a small hole in the tray. I can only guess that this is to allow the fuel in the very bottom of the tank to get to the pump.

As to the return line, if you dump it into the main part of the tank and run low on fuel, the fuel would have to migrate from the return line to the pump. Returning it directly to the sump keeps it topped off, IMO. I can't ever recall seeing a factory return line that runs anywhere but into the area near the pump.