From the documentation on the site:
"Each filter has a 12db/oct roll off and is used to set the upper cutoff point of the subwoofer. Normally, you will set both filters at the same frequency for a 24db/oct roll off. In some systems it may be advantageous to be able to independently adjust these filters for the optimum blend"
It appears they are there to provide added flexibility and to smooth out the crossover upper limit if there are issues. In other words you could creat a more gradual cuttoff of the sub if so desired