After the water transfers from the top reservoir to the boiler, the pump continues to run to aerate/percolate the water in the boiler.  This creates a mixing effect for the water in the boiler so that the water is perfectly (and consistently) heated throughout.  This is a huge advantage of the SWIRL system compared to other systems as they can have huge (20+ degree) gradient differences in temperature of the water in their boilers.  A predictable, target temperature is a key to making the best cup of coffee possible.