Yep... The designer had the refugium in the far right side... But he didn't want 100% of the flow going through the ref, so he tapped a line off the return to provide a controlled flow of freshly filtered water into the refugium. (The valve allows you to control exactly how much flow it gets.)
The drain going into the right side of the center box was the main drain... The one on the left side is the secondary/backup drain (taller standpipe in the display tank)... The center box is where the filter media/live rock would be; would be crowded, but that's where I'd put a skimmer too. (Or a HOB
skimmer on the side of the sump would leave more room for LR
in the sump.)
If that set-up suits your needs/tastes then no need to change anything.