I haven't used a Behringer, but the SMS-1 was designed from the ground up to deal with frequencies below 100Hz. The Auto-EQ options are something of a convenience: they'll adjust EQ levels to do the best they can at the default frequency settings and Q settings (and whatever level and phase you set the unit to before running the auto mode). It's the manual adjustments that really let the SMS-1 shine. Unlike the Behringer, the SMS-1 adds the ability to accurately measure the SPL from the frequency sweep and to display that on your TV. Check out the example at the end of Outlaw's guide to see just what the SMS-1 can do.

On the other hand... The SMS-1 is a mono device - if you want to use it to EQ your mains at 100Hz, you'd need one for each channel. I actually moved my crossover for my mains up from 60Hz to 80Hz because I found a null in the low 60's and shifting the crossover up alowed me to fix it with the SMS-1. I agree that fixing a 100Hz mode is a somewhat different matter, though.