Short Answer: The scaling factor reflects the electrode spacing (only in 2D files) when you use a unit spacing of 1 between electrodes in your command file geometry.
Long Answer: When writing a command file (geometry section), it is a good idea to use a unit spacing of 1 between electrodes. This is so the file can be used for any electrode spacing by simply changing the scaling factor in the SuperSting™ Data File Setup Menu (see image below). By having 1 unit spacing, the scaling factor simply reflects the new electrode spacing. Only one command file for 2D needs to be loaded for each electrode array type used, even if different electrode spacings will be used later on. 3D command files have XYZ spacing set ahead of time and do not use a scaling factor. In this 2D example below, the operators would be deploying 1m. It is best to enter the true scaling factor value in the SuperSting menu shown below for 2D files because the field operator is person setting the electrodes and any deviation from plans would be accounted for in this menu below. Rescaling later in EarthImager2D may produce errors in the office if the spacing was not communicated correctly.