I agree, there is no way you can compare identical scrubbers on 2 different tanks due to the reasons you described. It would be near impossible to have identical results on 2 different display tanks.
As for the slot, yes, it is algae coming from my display getting stuck inside the pipe. I have this fern looking algae growing in my display that I pull out handfuls each week. I pull out as much out of the display as I clean off the screen each week. I try and remove as much as I can but a few pieces get pulled into the overflow, in turn getting stuck in the pipe and causing flow issues. Thinking about it more, I don't see how making the slot a little bigger would help because these are large chunks of algae getting in the pipe and I would have to widen the slot way to much in order for this type of algae to pass through, so I will probably just have to wait it out until the algae in my display is gone, then I will not have any more flow issues. When I clean the screen and pipe each week the flow is perfect over the entire screen right after I clean it.