I'll take a stab at it... i'm sure others will join. Even though I've got good circulation, there are dead spots where fish waste hangs out. And by keeping these clean as well as the little crevices that are found in the LR, you avoid spots where algae could grow. Basically, you're getting excess nutrients into the water column so that you can either filter them out (before the water dumps into my sump, I've got a little fiber-filter that I wash out regularly), but it also lets the skimmer pick up stuff too.
It also simulates what would happen if the reef got a rough patch of weather, and things get blown around a bit to "clean" the reef.
What wings said plus with a power head you can keep some of the gunk from accumulating in the LR. Hit a hole in the LR and you will be surprised and what and through how many holes things come out.