The problem with the scenario quoted in the original post is not with starting the aircraft with a flat battery, it is with taking off with a flat battery. It takes a while for the battery to recharge and if the aircraft suffered an electrical generation failure in flight, would the battery have sufficient power to supply essential services until landing if it was not fully charged yet? Possibly in VFR conditions but if the aircraft had to return to an instrument approach, one would be slightly embarrassed if the "off" flags started dropping in half way down the ILS.