Setting it to "bypass" would skip the digital section and bass management, at which point the LSi9's -3dB point of 50Hz would yield some measurable output down into the 40's. If you are in "stereo" mode you will still have the bass management in place, but there would be some output from the speakers even still.

I'd want to do the SMS-1 setup with the actual crossover that you will use. The purpose of the SMS-1 is to achieve a flat frequency response in the low frequencies - not just flat from the sub, but flat from the overall system of sub and speakers. The LSi9's will contribute something to the output below 100Hz, so you should let yourself include that contribution in the overall calibration.