It makes references to the zerro suppression method you choosed when you generated the Excellon file. Flatcam does not know automatically what method you used so you have to tell the software (FlatCam) if the leading zeros were removed or if the trailing zeros were the ones removed. In this way FlatCam knows how to interpret the data in the Excellon file.
I also cannot do set_sys excellon_zeroes T in the development version. However, in the stable version it is done normally.
There is a small bug in the dev version. It's missing an "else" keyword in a "if" statement.