Greg, I'm getting loopy trying to follow your loops
I run all scrubbers on dedicated pumps. I didn't always, but it's safer. The reason is not the algae clogging anything, it's something getting into the plumbing and stopping up the slot pipe from the inside. Snail, anemone, etc.
Ok so if you want to minimize pumps then you need to have a dual overflow system, and you need to tune it such that 100% of the flow can go through the path that the scrubber is not on. If you only have one overflow, then you need to create a bypass. This is rather simple but must be thought out so that it allows full bypass flow in the event of a 100% clog, without causing a tank overflow AND without allowing the bypass pathway to let water through it under normal operation.
Basically, it's a pipe loop that tees off before the scrubber, rises up as high as possible (up the back side of the tank, if possible) then into a open tee and back down. This allows head pressure from the overflow pipe to 'build' on top of the slot/screen junction and keep the scrubber working. The slot has a variable head pressure throughout the weekly growth cycle, so towards the end, you might be maintaining a few feet of head in the overflow pipe because of algae wanting to grow into the slot/screen junction. The head pressure prevents this from happening, and you want the head pressure. If your bypass is too low in relation to the level of the slot pipe, your extra head pressure will go right by the scrubber and your screen will eventually get zero flow and die.
Here are a few hand sketches I made a while back to explain this concept.
The first pic might be for a single-level system. The second one was one I sketched up for someone with a basement sump.