Unfortunately I don't remember the tour specifics well enough to confirm the exact use case of the system.
It's an impressive system but there are definitely still storms large enough to overwhelm it. But, combined with the other flood defenses in the area, it has made flooding less common in all normal weather scenarios, which is a big win compared to the situation before it was built.
The rate given for the Edo Discharge Channel pumps in the article is 200 tons per second. At 5cm/hr, that's enough to drain a region 150km x 100 km, or the whole Tokyo metropolitan area.
There are other drains (like the Edo River itself) and other sources of rainfall, but based on that calculation 200 tons per second is a huge contributor to draining even a megacity.