Strictly speaking, the purpose of the gain switches is to adjust the pedal to the input and output signals needed. But, if you have a low output guitar, you may prefer the gain boost you get by going in guitar and coming out line. Or not.
If you want to achieve this in a live situation you can adjust the preset output level to boost the gain by 6 dB where desired – this is about the same as the output level switch. See UM p.16