Well, that baffle isn't necessary, but what it does is keep your pump from completely draining the sump in the event your drain pipes from the tank get clogged. The pump will only drain that last compartment after the baffle. This can ensure that at least some of the media at the bottom of the biochamber will remain wet/submerged until water flow is restored through the system. If all of the biomedia were to completely dry out, then you would lose all of it. This way its likely to last at least a little bit longer.
But it will also cause you to have bubbles pumped into your tank from the turbulence caused by the water falling over a baffle immediately before your pump(s).