Manual states it's for Height or Presence speaker measurements. So if you're not running Atmos or don't have Presence speakers, don't even worry about it. I can't really say if it would make any improvement with surround sound because I am not running Atmos. Just place the mic on a tripod, measure up and start enjoying!
And yes, the "through" mode sounds best most of the time, to me anyway. Sometimes I do you use the "natural" setting though. Very nice piece of gear by the way! I do enjoy mine.